Sali Lab logo Laboratory of Andrej Sali QB3

Publications

476.B. Raveh, R. Eliasian, S. Rashkovits, D. Russel, R. Hayama, S. Sparks, D. Singh, R.Y.H. Lim, E. Villa, M.P. Rout, D. Cowburn, A. Sali. Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport. Proc Natl Acad Sci U S A 122, e2507559122, 2025. PMCID12557478 PubMed
475.A.O. Zalevsky, B. Vallat, B.M. Webb, H. Tangmunarunkit, M.R. Sekharan, A. Shafaeibejestan, S. Ganesan, J. Sagendorf, C.M. Jeffries, J. Trewhella, A. Graziadei, J.A. Vizcaíno, A. Leitner, J. Rappsilber, E. Peisach, J.W. Flatt, J.Y. Young, K. Majila, S. Viswanath, C. Kesselman, J.C. Hoch, G. Kurisu, K.L. Morris, S. Velankar, H.M. Berman, S.K. Burley, A. Sali. IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank. J Mol Biol, in press, 2025.PDF
474.B. Vallat, Y. Rose, D.W. Piehl, J.M. Duarte, S. Bittrich, C. Bi, J. Segura, A. Zalevsky, M.R. Sekharan, B.M. Webb, C. Bhikadiya, M. Voigt, J. Henry, H. Chao, A. Pingale, D. Raymond, J. Sagendorf, E. Peisach, Z. Feng, V. Guranovic, J. Smith, A.S. Rose, J.Y. Young, H.M. Berman, A. Sali, S.K. Burley. RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models. Nucleic Acids Res, 2025. PMCID12807596 PubMedPDF
473.M.S. Taylor, M. Chen, M. Hancock, M. Wranik, B.D. Miller, T.R. O’Meara, B.A. Palanski, S.B. Ficarro, B.J. Groendyke, Y. Xiang, K.T. Kondo, K.Y. Linde-Garelli, M.J. Lee, D. Mondal, D. Freund, S. Congreve, K. Matas, M. Hennink, K. Xibinaku, M.L. Valenstein, T. van Eeuwen, J.A. Marto, A. Sali, Y. Shi, N.S. Gray, D.M. Sabatini, N. Chu, K.B. Rogala, P.A. Cole. Structural Basis for the Recruitment and Selective Phosphorylation of Akt by mTORC2. Science, in press, 2025.
472.G. Tauriello, Y. Lill, J. Sgrignani, V. Zoete, B. Singer, B. Vallat, B.M. Webb, T. Garello, S. Bienert, M. Feig, S.K. Burley, A. Sali, M.A. Lill, A. Cavalli, M. Dal Peraro, T. Schwede. ModelCIF update: Supporting Emerging Classes of Computational Macromolecular Models. J Mol Biol, in press, 2025.
471.T. Kozai, J. Fernandez-Martinez, L.E. Kapinos, P. Gallardo, T. van Eeuwen, M. Saladin, R. Eliasian, A. Mazur, W. Zhang, J. Tempkin, R. Panatala, M. Delgado-Izquierdo, R. Escribano-Marin, Q. Feng, C. Lin, A. Sali, B.T. Chait, B. Raveh, L.M. Veenhoff, M.P. Rout, R.Y.H. Lim. Karyopherins Remodel the Dynamic Organization of the Nuclear Pore Complex Transport Barrier. Nat Cell Biol, 2025.PDF
470.M. Hancock, J. Holton, J.S. Fraser, P.D. Adams, A. Sali. Bayesian multi-state multi-condition modeling of a protein structure from X-ray crystallography. bioRxiv, in press, 2025. bioRxiv
469.A. Biswas, I. Choudhuri, K. Huang, Q. Sun, A. Sali, I. Echeverria, A. Haldane, R.M. Levy, D. Lyumkis. Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV. bioRxiv, in press, 2025. PMCID12073831 PubMed
468.L.V. Schaffer, M. Hu, G. Qian, K.M. Moon, A. Pal, N. Soni, A.P. Latham, L. Pontano Vaites, D. Tsai, N.M. Mattson, K. Licon, R. Bachelder, A. Cesnik, I. Gaur, T. Le, W. Leineweber, A. Palar, E. Pulido, Y. Qin, X. Zhao, C. Churas, J. Lenkiewicz, J. Chen, K. Ono, D. Pratt, P. Zage, I. Echeverria, A. Sali, J.W. Harper, S.P. Gygi, L.J. Foster, E.L. Huttlin, E. Lundberg, T. Ideker. Multimodal cell maps as a foundation for structural and functional genomics. Nature, 2025. PMCID12137143 PubMedPDF
467.S.V. Shenoy, D. Biswas, K. Mandal, A. Zalevsky, A. Kishishita, A. Verma, I. Upadhay, Y. He, A. Sali, R. Viner, S. Srivastava, A.P. Wiita. AlphaCross-XL: a seamless tool for automated and proteome-scale mapping of crosslinked peptides onto three-dimensional protein structures. bioRxiv, 2025. bioRxiv
466.N.K. Khandelwal, M. Gupta, J.E. Gomez, S. Barkho, Z. Guan, A.Y. Eng, T. Kawate, S.G. Balasubramani, A. Sali, D.T. Hung, R.M. Stroud. Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A. Nat Comm 16, 3139, 2025. PMCID11961569 PubMedPDF
465.A.P. Latham, M. Rožič, B.M. Webb, A. Sali. Tutorial on integrative spatiotemporal modeling by integrative modeling platform. Protein Sci 34, e70107, 2025. PMCID11934212 PubMedPDF
464.N.E. Ketaren, P.C. Fridy, V. Malashkevich, T. Sanyal, M. Brillantes, M.K. Thompson, D.A. Oren, J.B. Bonanno, A. Šali, S.C. Almo, B.T. Chait, M.P. Rout. Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies. Structure 33, 677-690.e5, 2025. PMCID12042621 PubMedPDF
463.B. Vallat, B.M. Webb, A. Zalevsky, H. Tangmunarunkit, M.R. Sekharan, S. Voinea, A. Shafaeibejestan, J. Sagendorf, J.C. Hoch, G. Kurisu, K.L. Morris, S.V. Velankar, C. Kesselman, S.K. Burley, H.M. Berman, A. Sali. PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures. J Mol Biol 437, 168963, 2025. PMCID12327472 PubMedPDF
462.A.P. Latham, W. Zhang, J.O.B. Tempkin, S. Otsuka, J. Ellenberg, A. Sali. Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex. Proc Natl Acad Sci USA 122, e2415674122, 2025. PMCID11929490 PubMedPDF
461.T.O. Peulen, K. Hemmen, A. Greife, B.M. Webb, S. Felekyan, A. Sali, C.A.M. Seidel, H. Sanabria, K.G. Heinze. tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling. Bioinformatics 41, btaf025, 2025. PMCID11796090 PubMedPDF
460.D. Mondal, V. Kumar, T. Satler, R. Ramachandran, D. Saltzberg, I. Chemmama, K.B. Pilla, I. Echeverria, B.M. Webb, M. Gupta, K.A. Verba, A. Sali. Recognizing amino acid sidechains in a medium resolution cryo-electron density map. Prot Sci 34, e70217, 2025. PMCID12302279 PubMedPDF
459.D. Scholl, T. Boyd, A.P. Latham, A. Salazar, A. Khan, S. Boeynaems, A.S. Holehouse, G.C. Lander, A. Sali, D. Park, A.A. Deniz, K. Lasker. Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure. bioRxiv, 2024. bioRxiv
458.C.A. Hanke, J.D. Westbrook, B.M. Webb, T. Peulen, C.L. Lawson, A. Sali, H.M. Berman, C.A.M. Seidel, B. Vallat. Making fluorescence-based integrative structures and associated kinetic information accessible. Nat Meth 21, 1970-1972, 2024. PMCID11939118 PubMedPDF
457.T. Clark, J. Mohan, L. Schaffer, K. Obernier, S. Al Manir, C.P. Churas, A. Dailamy, Y. Doctor, A. Forget, J.N. Hansen, M. Hu, J. Lenkiewicz, M.A. Levinson, C. Marquez, S. Nourreddine, J. Niestroy, D. Pratt, G. Qian, S. Thaker, J. Bélisle-Pipon, C. Brandt, J. Chen, Y. Ding, S. Fodeh, N. Krogan, E. Lundberg, P. Mali, P. Payne-Foster, S. Ratcliffe, V. Ravitsky, A. Sali, W. Schulz, T. Ideker. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. in press, 2024. PMCID11142054 PubMed bioRxiv
456.S.W. Yee, L.F. Peral, P. Alentorn-Moron, C. Fontsere, M. Ceylan, M. Koleske, N. Handin, V. Artegoitia, G. Lara, H. Chien, X. Zhou, J. Dainat, A. Zalevsky, A. Sali, C. Brand, F. Wolfreys, J. Yang, J. Gestwicki, J. Capra, P. Artursson, J. Newman, T. Marques-Bonet, K. Giacomini. Illuminating the Function of the Orphan Transporter, SLC22A10, in Humans and Other Primates. Nat Comm 15, 4380, 2024. PMCID11116522 PubMedPDF
455.D. Singh, N. Soni, J. Hutchings, I. Echeverria, F. Shaikh, M. Duquette, S. Suslov, Z. Li, T. van Eeuwen, K. Molloy, Y. Shi, J. Wang, Q. Guo, B.T. Chait, J. Fernandez-Martinez, M.P. Rout, A. Sali, E. Villa. The Molecular Architecture of the Nuclear Basket. Cell 187, 5267-5281, 2024. PMCID11416316 PubMedPDF
454.B. Vallat, B.M. Webb, J.D. Westbrook, T.D. Goddard, C.A. Hanke, A. Graziadei, E. Peisach, A. Zalevsky, J. Sagendorf, H. Tangmunarunkit, S. Voinea, M. Sekharan, J. Yu, A.A.M.J.J. Bonvin, F. DiMaio, G. Hummer, J. Meiler, E. Tajkhorshid, T.E. Ferrin, C.L. Lawson, A. Leitner, J. Rappsilber, C.A.M. Seidel, C.M. Jeffries, S.K. Burley, J.C. Hoch, G. Kurisu, K. Morris, A. Patwardhan, S. Velankar, T. Schwede, J. Trewhella, C. Kesselman, H.M. Berman, A. Sali. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol 436, 168546, 2024. PMCID11377171 PubMedPDF
453.B. Raveh, R. Eliasian, S. Rashkovits, D. Russel, R. Hayama, S.E. Sparks, D. Singh, R. Lim, E. Villa, M.P. Rout, D. Cowburn, A. Sali. Integrative spatiotemporal map of nucleocytoplasmic transport. in press, 2024. PMCID10802240 PubMed bioRxiv
452.W. Li, A. Li, B. Yu, X. Zhang, X. Liu, K.L. White, R.C. Stevens, W. Baumeister, A. Sali, M. Jasnin, L. Sun. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Nat Commun 15, 1311, 2024. PMCID10861521 PubMedPDF
451.S. Pourmal, E. Green, R. Bajaj, I. Chemmama, G.M. Knudsen, M. Gupta, A. Sali, Y. Cheng, C.S. Craik, R.M. Stroud, D.L. Kroetz. Structural Basis of Prostaglandin Efflux by MRP4. Nat Struct Mol Biol 31, 621-632, 2024. PMCID11145372 PubMedPDF
450.N.E. Ketaren, F.D. Mast, P.C. Fridy, J.P. Olivier, T. Sanyal, A. Sali, B.T. Chait, M.P. Rout, J.D. Aitchison. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. eLife 12, RP89423, 2024. PMCID11076045 PubMedPDF
448.Z. Lin, K. Schaefer, I. Lui, Z. Yao, A.A. Fossati, D.L. Swaney, A. Palar, A. Sali, J.A. Wells. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science 385, eadl5763, 2024. PMCID12517702 PubMedPDF
447.E.T. Baldwin, T. van Eeuwen, D. Hoyos, A. Zalevsky, E.P. Tchesnokov, R. Sánchez, B.D. Miller, L.H. Di Stefano, F.X. Ruiz, M. Hancock, E. Işik, C. Mendez-Dorantes, T. Walpole, C. Nichols, P. Wan, K. Riento, R. Halls-Kass, M. Augustin, A. Lammens, A. Jestel, P. Upla, K. Xibinaku, S. Congreve, M. Hennink, K.B. Rogala, A.M. Schneider, J.E. Fairman, S.M. Christensen, B. Desrosiers, G.S. Bisacchi, O.L. Saunders, N. Hafeez, W. Miao, R. Kapeller, D.M. Zaller, A. Sali, O. Weichenrieder, K.H. Burns, M. Götte, M.P. Rout, E. Arnold, B.D. Greenbaum, D.L. Romero, J. LaCava, M.S. Taylor. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature 626, 194-206, 2023. PMCID10830420 PubMedPDF
446.T.O. Peulen, A. Sali. Bayesian Fluorescence Framework for integrative modeling of biomolecules. in press, 2023. bioRxiv
445.C.W. Akey, I. Echeverria, C. Ouch, I. Nudelman, Y. Shi, J. Wang, B.T. Chait, A. Sali, J. Fernandez-Martinez, M.P. Rout. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell 83, 3283-3302.e5, 2023. PMCID10630966 PubMedPDF
444.S.K. Kim, M.S. Dickinson, J. Finer-Moore, Z. Guan, R.M. Kaake, I. Echeverria, J. Chen, E.H. Pulido, A. Sali, N.J. Krogan, O.S. Rosenberg, R.M. Stroud. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol 30, 296-308, 2023. PMCID10312659 PubMedPDF
443.K.H. Burns, B. Smail, H. Jiang, A. Zalevsky, N. Dai, R.J. Trachman, S. Guan, A. Sali, M.S. Taylor, J. LaCava. Robust cleavage of mismatched DNA by the LINE-1 endonuclease. J Biol Chem, in press, 2023.
442.T. Kozai, J. Fernandez-Martinez, T. van Eeuwen, P. Gallardo, L.E. Kapinos, A. Mazur, W. Zhang, J. Tempkin, M. Delgado-Izquierdo, B. Raveh, A. Sali, B.T. Chait, L.M. Veenhoff, M.P. Rout, R.Y.H. Lim. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. in press, 2023. PMCID10103940 PubMed bioRxiv
441.B. Vallat, G. Tauriello, S. Bienert, J. Haas, B.M. Webb, A. Žídek, W. Zheng, E. Peisach, D.W. Piehl, I. Anischanka, I. Sillitoe, J. Tolchard, M. Varadi, D. Baker, C. Orengo, Y. Zhang, J.C. Hoch, G. Kurisu, A. Patwardhan, S. Velankar, S.K. Burley, A. Sali, T. Schwede, H.M. Berman, J.D. Westbrook. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. J Mol Biol 435, 168021, 2023. PMCID10293049 PubMedPDF
440.S. Otsuka, J.O.B. Tempkin, W. Zhang, A.Z. Politi, A. Rybina, M.J. Hossain, M. Kueblbeck, A. Callegari, B. Koch, N.R. Morero, A. Sali, J. Ellenberg. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature 613, 575-581, 2023. PMCID9849139 PubMedPDF
439.I. Echeverria, H. Braberg, N.J. Krogan, A. Sali. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J 290, 2565-2575, 2023. PMCID9481981 PubMedPDF
438.S.K. Burley, H.M. Berman, W. Chiu, W. Dai, J.W. Flatt, B.P. Hudson, J.T. Kaelber, S.D. Khare, A.W. Kulczyk, C.L. Lawson, G.D. Pintilie, A. Sali, B. Vallat, J.D. Westbrook, J.Y. Young, C. Zardecki. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev 14, 1281-1301, 2022. PMCID9715422 PubMedPDF
437.S.K. Burley, H.M. Berman, J.M. Duarte, Z. Feng, J.W. Flatt, B.P. Hudson, R. Lowe, E. Peisach, D.W. Piehl, Y. Rose, A. Sali, M. Sekharan, C. Shao, B. Vallat, M. Voigt, J.D. Westbrook, J. Young, C. Zardecki. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 12, 1425, 2022. PMCID9599165 PubMedPDF
436.K.A. Opoku-Nsiah, A.H. de la Pena, S.K. Williams, N. Chopra, A. Sali, G.C. Lander, J.E. Gestwicki. The YΦ Motif Defines the Structure-Activity Relationships of Human 20S Proteasome Activators. Nat Commun 13, 1226, 2022. PMCID8907193 PubMedPDF
435.S. Burley, C. Bhikadiya, C. Bi, S. Bittrich, H. Chao, L. Chen, P. Craig, G. Crichlow, K. Dalenberg, J.M. Duarte, S. Dutta, M. Fayazi, Z. Feng, J. Flatt, S. Ganesan, S. Ghosh, D. Goodsell, R.K. Green, V. Guranovic, J. Henry, B. Hudson, C. Lawson, Y. Liang, R. Lowe, E. Peisach, I. Persikova, D. Piehl, Y. Rose, A. Sali, J. Segura, M. Sekharan, C. Shao, B. Vallat, M. Voigt, B. Webb, J. Westbrook, S. Whetstone, J. Young, A. Zalevsky, C. Zardecki. RCSB Protein Data Bank: Tools for visualizing and understanding biological macromolecules in 3D. Prot Sci 31, e4482, 2022. PMCID9667899 PubMedPDF
434.A. Li, X. Zhang, J. Singla, K. White, V. Loconte, C. Hu, C. Zhang, S. Li, W. Li, J.P. Francis, C. Wang, A. Sali, L. Sun, X. He, R.C. Stevens. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. PLoS One 17, e0265567, 2022. PMCID8947144 PubMedPDF
433.A. Rafiei, L. Lee, D.A. Crowder, D.J. Saltzberg, A. Sali, G.J. Brouhard, D.C. Schriemer. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 11, e66975, 2022. PMCID9122500 PubMedPDF
432.A. Guo, J. Zhang, B. He, A. Li, T. Sun, C. Li, J. Wang, R. Tai, J. Fan, A. Sali, R.C. Stevens, H. Jiang. Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic β cells. Proc Natl Acad Sci USA 119, e2202695119, 2022. PMCID9371705 PubMedPDF
431.M. Hancock, T.O. Peulen, B. Webb, B. Poon, J.S. Fraser, P. Adams, A. Sali. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol 214, 107841, 2022. PMCID9278553 PubMedPDF
430.V. Loconte, J. Singla, A. Li, J.H. Chen, A. Ekman, G. McDermott, A. Sali, M. Le Gros, K.L. White, C.A. Larabell. Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure 30, 510-521, 2022. PMCID9013509 PubMedPDF
429.K.D. Belsare, H. Wu, D. Mondal, A. Bond, E. Castillo, J. Jin, H. Jo, A.E. Roush, K.B. Pilla, S. Sali, C. Condello, W.F. DeGrado. Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ. Proc Natl Acad Sci USA 119, e2114486119, 2022. PMCID8812518 PubMedPDF
428.H. Braberg, I. Echeverria, R. Kaake, A. Sali, N. Krogan. From systems to structure — using genetic data to model protein structures. Nat Rev Genet 23, 342-354, 2022. PMCID8744059 PubMedPDF
427.C.W. Akey, D. Singh, C. Ouch, I. Echeverria, I. Nudelman, J.M. Varberg, Z. Yu, F. Fang, Y. Shi, J. Wang, D. Salzberg, K. Song, C. Xu, J.C. Gumbart, S. Suslov, J. Unruh, S.L. Jaspersen, B.T. Chait, A. Sali, J. Fernandez-Martinez, S.J. Ludtke, E. Villa, M.P. Rout. Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex. Cell 185, 361-378, 2022. PMCID8928745 PubMedPDF
426.S.K. Burley, C. Bhikadiya, C. Bi, S. Bittrich, H. Chao, L. Chen, P.A. Craig, G.V. Crichlow, K. Dalenberg, J.M. Duarte, S. Dutta, M. Fayazi, Z. Feng, J.W. Flatt, S. Ganesan, S. Ghosh, D.S. Goodsell, R.K. Green, V. Guranovic, J. Henry, B.P. Hudson, I. Khokhriakov, C.L. Lawson, Y. Liang, R. Lowe, E. Peisach, I. Persikova, D.W. Piehl, Y. Rose, A. Sali, J. Segura, M. Sekharan, C. Shao, B. Vallat, M. Voigt, B. Webb, J.D. Westbrook, S. Whetstone, J.Y. Young, A. Zalevsky, C. Zardecki, S.K. Burley, C. Bhikadiya, C. Bi, S. Bittrich, L. Chen, G.V. Crichlow, J.M. Duarte, S. Dutta, M. Fayazi, Z. Feng, J.W. Flatt, S.J. Ganesan, D.S. Goodsell, S. Ghosh, R.K. Green, V. Guranovic, J. Henry, B.P. Hudson, C.L. Lawson, Y. Liang, R. Lowe, E. Peisach, I. Persikova, D.W. Piehl, Y. Rose, A. Sali, J. Segura, M. Sekharan, C. Shao, B. Vallat, M. Voigt, J.D. Westbrook, S. Whetstone, J.Y. Young, C. Zardecki. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Prot Sci 31, 187-208, 2022. PMCID8740825 PubMedPDF
425.A. Li, S. Zhang, V. Loconte, Y. Liu, A. Ekman, G.J. Thompson, A. Sali, R.C. Stevens, K. White, J. Singla, L. Sun. An Intensity-based Post-processing Tool for 3D Instance Segmentation of Organelles in Soft X-ray Tomograms. PLoS One 17, e0269887, 2022. PMCID9436087 PubMedPDF
424.F. Huang, T.T.T. Nguyen, I. Echeverria, R. Ramachandran, D.C. Cary, H. Paculova, A. Sali, A. Weiss, B.M. Peterlin, K. Fujinaga. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. eLife 10, e68473, 2021. PMCID8648303 PubMedPDF
423.D.S. Ziemianowicz, D. Saltzberg, T. Pells, D.A. Crowder, C. Schräder, M. Hepburn, A. Sali, D.C. Schriemer. IMProv: A Resource for Crosslink-Driven Structure Modeling that Accommodates Protein Dynamics. Mol Cell Prot 20, 100139, 2021. PMCID8452774 PubMedPDF
422.R.M. Kaake, I. Echeverria, S.J. Kim, J. Von Dollen, N.M. Chesarino, Y. Feng, C. Yu, H. Ta, L. Chelico, L. Huang, J. Gross, A. Andrej Sali, N.J. Krogan. Characterization of a A3G-VifHIV-1-CRL5-CBFβ structure using a cross-linking mass spectrometry pipeline for integrative modeling of host-pathogen complexes. Mol Cell Prot 20, 100132, 2021. PMCID8459920 PubMedPDF
421.A. Sali. From integrative structural biology to cell biology. J Biol Chem, 100743, 2021. PMCID8203844 PubMedPDF
420.B. Vallat, B. Webb, M. Fayazi, S. Voinea, H. Tangmunarunkit, S.J. Ganesan, C.L. Lawson, J.D. Westbrook, C. Kesselman, A. Sali, H.M. Berman. New system for archiving integrative structures. Acta Cryst D 77, 1486-1496, 2021. PMCID8647179 PubMedPDF
419.B. Webb, A. Sali. Protein Structure Modeling with MODELLER. Meth Mol Biol 2199, 239-255, 2021. PubMedPDF
418.M. Hepburn, D.J. Saltzberg, L. Lee, S. Fang, C. Atkinson, N.C.J. Strynadka, A. Sali, S.P. Lees-Miller, D.C. Schriemer. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure 29, 1-12, 2021. PMCID8675206 PubMedPDF
417.F.D. Mast, P.C. Fridy, N.E. Ketaren, J. Wang, E.Y. Jacobs, J.P. Olivier, T. Sanyal, K.R. Molloy, F. Schmidt, M. Rutkowska, Y. Weisblum, L.M. Rich, E.R. Vanderwall, N. Dambrauskas, V. Vigdorovich, S. Keegan, J.B. Jiler, M.E. Stein, P.D.B. Olinares, L. Herlands, T. Hatziioannou, D.N. Sather, J.S. Debley, D. Fenyö, A. Sali, P.D. Bieniasz, J.D. Aitchison, B.T. Chait, M.P. Rout. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. eLife 10, e73027, 2021. PMCID8043454 PubMedPDF
416.A. Brilot, A. Lyon, A. Zelter, S. Viswanath, A. Maxwell, K.C.B. Yabut, M. MacCoss, E. Eric Muller, A. Sali, T.N. Davis, D.A. Agard. CM1-driven assembly and activation of Yeast γ-Tubulin Small Complex underlies microtubule nucleation. eLife 10, e65168, 2021. PMCID8099430 PubMedPDF
415.B. Raveh, L. Sun, K.L. White, T. Sanyal, J. Tempkin, D. Zheng, K.B. Pilla, J. Singla, C. Wang, J. Zha, A. Li, N.A. Graham, C. Kesselman, R.C. Stevens, A. Sali. Bayesian metamodeling of complex biological systems across varying representations. Proc Natl Acad Sci USA 118, e2104559118, 2021. PMCID8536362 PubMedPDF
414.Y. Yu, S. Li, Z. Ser, T. Sanyal, K. Choi, B. Wan, H. Kuang, A. Sali, A. Kentsis, D.J. Patel, X. Zhao. Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Proc. Natl. Acad. Sci. 118, e2026844118, 2021. PMCID8126833 PubMedPDF
413.E.C. Salcedo, M.B. Winter, N. Khuri, G.M. Knudsen, A. Sali, C.S. Craik. Global Protease Activity Profiling Identifies HER2-Driven Proteolysis in Breast Cancer. ACS Chem. Biol. 16, 712-723, 2021. PubMedPDF
412.D.J. Saltzberg, S. Viswanath, I. Echeverria, I.E. Chemmama, B. Webb, A. Sali. Using Integrative Modeling Platform to Compute, Validate, and Archive a Model of a Protein Complex Structure. Prot Sci 30, 250-261, 2021. PMCID7737781 PubMedPDF
411.S.K. Burley, C. Bhikadiya, C. Bi, S. Bittrich, L. Chen, G. Crichlow, C.H. Christie, K. Dalenberg, L. Di Costanzo, J.M. Duarte, S. Dutta, Z. Feng, S. Ganesan, D.S. Goodsell, S. Ghosh, R.K. Green, V. Guranović, D. Guzenko, B.P. Hudson, C.L. Lawson, Y. Liang, R. Lowe, H. Namkoong, E. Peisach, I. Persikova, C. Randle, A. Rose, Y. Rose, A. Sali, J. Segura, M. Sekharan, C. Shao, Y. Tao, M. Voigt, J.D. Westbrook, J.Y. Young, C. Zardecki, M. Zhuravleva. RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering, and energy sciences. Nucleic Acids Res 49, D437-D451, 2021. PMCID7779003 PubMedPDF
410.T.H. Tran, J.V. Nguyen, A. Stecula, J. Akutagawa, A.V. Moorman, B.S. Braun, A. Sali, C.G. Mullighan, N.P. Shah, Y. Dai, M. Devidas, K.G. Roberts, C.C. Smith, M.L. Loh. The EBF1-PDGFRB T681I mutation is highly resistant to imatinib and dasatinib in vitro and detectable in clinical samples prior to treatment. Haematologica 106, 2242-2245, 2021. PMCID8327742 PubMedPDF
409.D.E. Gordon, J. Hiatt, M. Bouhaddou, V.V. Rezelj, S. Ulferts, H. Braberg, A.S. Jureka, K. Obernier, J.Z. Guo, J. Batra, R.M. Kaake, A.R. Weckstein, T.W. Owens, M. Gupta, S. Pourmal, E.W. Titus, M. Cakir, M. Soucheray, M. McGregor, Z. Cakir, G. Jang, M.J. O'Meara, T.A. Tummino, Z. Zhang, H. Foussard, A. Rojc, Y. Zhou, D. Kuchenov, R. Hüttenhain, J. Xu, M. Eckhardt, D.L. Swaney, J.M. Fabius, M. Ummadi, B. Tutuncuoglu, U. Rathore, M. Modak, P. Haas, K.M. Haas, Z.Z.C. Naing, E.H. Pulido, Y. Shi, I. Barrio-Hernandez, D. Memon, E. Petsalaki, A. Dunham, M.C. Marrero, D. Burke, C. Koh, T. Vallet, J.A. Silvas, C.M. Azumaya, C. Billesbølle, A.F. Brilot, M.G. Campbell, A. Diallo, M.S. Dickinson, D. Diwanji, N. Herrera, N. Hoppe, H.T. Kratochvil, Y. Liu, G.E. Merz, M. Moritz, H.C. Nguyen, C. Nowotny, C. Puchades, A.N. Rizo, U. Schulze-Gahmen, A.M. Smith, M. Sun, I.D. Young, J. Zhao, D. Asarnow, J. Biel, A. Bowen, J.R. Braxton, J. Chen, C.M. Chio, U.S. Chio, I. Deshpande, L. Doan, B. Faust, S. Flores, M. Jin, K. Kim, V.L. Lam, F. Li, J. Li, Y.L. Li, Y. Li, X. Liu, M. Lo, K.E. Lopez, A.A. Melo, F.R. Moss, P. Nguyen, J. Paulino, K.I. Pawar, J.K. Peters, T.H. Pospiech, M. Safari, S. Sangwan, K. Schaefer, P.V. Thomas, A.C. Thwin, R. Trenker, E. Tse, T.K.M. Tsui, F. Wang, N. Whitis, Z. Yu, K. Zhang, Y. Zhang, F. Zhou, D. Saltzberg, A.J. Hodder, A.S. Shun-Shion, D.M. Williams, K.M. White, R. Rosales, T. Kehrer, L. Miorin, E. Moreno, A.H. Patel, S. Rihn, M.M. Khalid, A. Vallejo-Gracia, P. Fozouni, C.R. Simoneau, T.L. Roth, D. Wu, M.A. Karim, M. Ghoussaini, I. Dunham, F. Berardi, S. Weigang, M. Chazal, J. Park, J. Logue, M. McGrath, S. Weston, R. Haupt, C.J. Hastie, M. Elliott, F. Brown, K.A. Burness, E. Reid, M. Dorward, C. Johnson, S.G. Wilkinson, A. Geyer, D.M. Giesel, C. Baillie, S. Raggett, H. Leech, R. Toth, N. Goodman, K.C. Keough, A.L. Lind, R.J. Klesh, K.R. Hemphill, J. Carlson-Stevermer, J. Oki, K. Holden, T. Maures, K.S. Pollard, A. Sali, D.A. Agard, Y. Cheng, J.S. Fraser, A. Frost, N. Jura, T. Kortemme, A. Manglik, D.R. Southworth, R.M. Stroud, D.R. Alessi, P. Davies, M.B. Frieman, T. Ideker, C. Abate, N. Jouvenet, G. Kochs, B. Shoichet, M. Ott, M. Palmarini, K.M. Shokat, A. García-Sastre, J.A. Rassen, R. Grosse, O.S. Rosenberg, K.A. Verba, C.F. Basler, M. Vignuzzi, A.A. Peden, P. Beltrao, N.J. Krogan, QCRG Consortium Structural, Zoonomia Consortium. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 370, 2020. PMCID7808408 PubMedPDF
408.K.L. White, J. Singla, V. Loconte, J.H. Chen, A. Ekman, L. Sun, X. Zhang, J.P. Francis, A. Li, W. Lin, K. Tseng, G. McDermott, F. Alber, A. Sali, C. Larabell, R.C. Stevens. Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Sci Adv 6, 2020. PMCID7725475 PubMedPDF
407.A. Leitner, A.M.J.J. Bonvin, C.H. Borchers, R.J. Chalkley, J. Chamot-Rooke, C.W. Combe, J. Cox, M. Dong, L. Fischer, M. Götze, F.C. Gozzo, A.J.R. Heck, M.R. Hoopmann, L. Huang, Y. Ishihama, A.R. Jones, N. Kalisman, O. Kohlbacher, K. Mechtler, R.L. Moritz, E. Netz, P. Novak, E. Petrotchenko, A. Sali, R.A. Scheltema, C. Schmidt, D. Schriemer, A. Sinz, F. Sobott, F. Stengel, K. Thalassinos, H. Urlaub, R. Viner, J.A. Vizcaíno, M.R. Wilkins, J. Rappsilber. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure 28, 1259-1268, 2020. PubMedPDF
406.H. Braberg, I. Echeverria, S. Bohn, P. Cimermancic, A. Shiver, R. Alexander, J. Xu, M. Shales, R. Dronamraju, S. Jiang, G. Dwivedi, D. Bogdanoff, K.K. Chaung, R. Hüttenhain, S. Wang, . Mavor, . D, R. Pellarin, D. Schneidman, J.S. Bader, J.S. Fraser, J. Morris, J.E. Haber, B.D. Strahl, C.A. Gross, J. Dai, J.D. Boeke, A. Sali, N.J. Krogan. Genetic interaction mapping informs integrative structure determination of protein complexes. Science 370, 2020. PMCID7946025 PubMedPDF
405.Y. Qiao, Z. Wang, F. Tan, J. Chen, J. Lin, J. Yang, H. Li, X. Wang, A. Sali, L. Zhang, G. Zhong. Enhancer Reprogramming within Pre-existing Topologically Associated Domains Promotes TGF-β-Induced EMT and Cancer Metastasis. Mol Ther 28, 2083-2095, 2020. PMCID7474343 PubMedPDF
404.F.D. Mast, A.T. Navare, A.M. van der Sloot, J. Coulombe-Huntington, M.P. Rout, N.S. Baliga, A. Kaushansky, B.T. Chait, A. Aderem, C.M. Rice, A. Sali, M. Tyers, J.D. Aitchison. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 219, 2020. PMCID7659715 PubMedPDF
403.Y. Kwon, R. Kaake, I. Echeverria, M. Suarez, M.K. Shamsabadi, C. Stoneham, P.W. Ramirez, J. Kress, R. Singh, A. Sali, N. Krogan, J. Guatelli, X. Jia. Structural Basis of CD4 Downregulation by HIV-1 Nef. Nat Struct Mol Biol, 2020. PMCID7483821 PubMedPDF bioRxiv
402.D.E. Gordon, G.M. Jang, M. Bouhaddou, J. Xu, K. Obernier, M.J. O’Meara, J.Z. Guo, D.L. Swaney, T.A. Tummino, R. Hüttenhain, R.M. Kaake, A.L. Richards, B. Tutuncuoglu, H. Foussard, J. Batra, K. Haas, M. Modak, M. Kim, P. Haas, B.J. Polacco, H. Braberg, J.M. Fabius, M. Eckhardt, M. Soucheray, M.J. Bennett, M. Cakir, M.J McGregor, Q. Li, Z.Z.C. Naing, Y. Zhou, S. Peng, I.T. Kirby, J.E. Melnyk, J.S. Chorba, K. Lou, S.A. Dai, W. Shen, Y. Shi, Z. Zhang, I. Barrio-Hernandez, D. Memon, C. Hernandez-Armenta, C.J.P. Mathy, T. Perica, K.B. Pilla, S.J. Ganesan, D.J. Saltzberg, R. Ramachandran, X. Liu, S.B. Rosenthal, L. Calviello, S. Venkataramanan, Y. Lin, S.A. Wankowicz, M. Bohn, R. Trenker, J.M. Young, D. Cavero, J. Hiatt, T. Roth, U. Rathore, A. Subramanian, J. Noack, M. Hubert, F. Roesch, T. Vallet, B. Meyer, K.M. White, L. Miorin, D. Agard, M. Emerman, D. Ruggero, A. García-Sastre, N. Jura, M. Zastrow, J. Taunton, O. Schwartz, M. Vignuzzi, C. d’Enfert, S. Mukherjee, M. Jacobson, H.S. Malik, D.G. Fujimori, T. Ideker, C.S. Craik, S. Floor, J.S. Fraser, J. Gross, A. Sali, T. Kortemme, P. Beltrao, K. Shokat, B.K. Shoichet, N.J. Krogan. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459-468, 2020. PMCID7431030 PubMedPDF bioRxiv
401.S.J. Ganesan, M.J. Feyder, I.E. Chemmama, F. Fang, M.P. Rout, B.T. Chait, Y. Shi, M. Munson, A. Sali. Integrative Structure and Function of the Yeast Exocyst Complex. Protein Sci 29, 1486-1501, 2020. PMCID7255525 PubMedPDF
400.C. Gutierrez, I.E. Chemmama, H. Mao, C. Yu, I. Echeverria, S.A. Block, S.D. Rychnovsky, N. Zheng, A. Sali, L. Huang. Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling. Proc Natl Acad Sci U S A 117, 4088-4098, 2020. PMCID7049115 PubMedPDF
399.D.J. Saltzberg, M. Hepburn, K.B. Pilla, D.C. Schriemer, S.P. Lees-Miller, T.L. Blundell, A. Sali. SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. Prog Biophys Mol Biol 147, 92-102, 2019. PMCID6903780 PubMedPDF
398.H.M. Berman, P.D. Adams, A.A. Bonvin, S.K. Burley, B. Carragher, W. Wah Chiu, F. DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, Jr. Phillips GN, T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshid, J. Trewhella, B. Vallat, S. Velankar, G.W. Vuister, B. Webb, J.D. Westbrook, K.L. White, A. Sali. Federating Structural Models And Data: Outcomes From A Workshop On Archiving Integrative Structures. Structure 27, 1745-1759, 2019. PMCID7108332 PubMedPDF
397.H. Wu, D.J. Saltzberg, H.T. Kratochvil, H. Jo, A. Sali, W.F. DeGrado. Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc 141, 7320-7326, 2019. PMCID6800148 PubMedPDF
396.B. Vallat, B. Webb, J. Westbrook, A. Sali, H.M. Berman. Archiving and Disseminating Integrative Structure Models. J Biomol NMR 73, 385-398, 2019. PMCID6692293 PubMedPDF
395.M.P. Rout, A. Sali. Principles for Integrative Structural Biology Studies. Cell 177, 1384-1403, 2019. PMCID6810593 PubMedPDF
394.D. Saltzberg, C.H. Greenberg, S. Viswanath, I. Chemmama, B. Webb, R. Pellarin, I. Echeverria, A. Sali. Modeling biological complexes using Integrative Modeling Platform. Methods Mol Biol 2022, 353-377, 2019. PubMedPDF
393.A. Padavannil, P. Sarkar, S.J. Kim, T. Cagatay, J. Jiou, C.A. Brautigam, D.R. Tomchick, A. Sali, S. D'Arcy, Y.M. Chook. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 8, e43630, 2019. PMCID6453568 PubMedPDF
392.S. Viswanath, A. Sali. Optimizing model representation for integrative structure determination of macromolecular assemblies. Proc Natl Acad Sci USA, pii: 201814649, 2018. PMCID6329962 PubMedPDF
391.M. Jishage, X. Yu, Y. Shi, S.J. Ganesan, W.Y. Chen, A. Sali, B.T. Chait, F.J. Asturias, R.G. Roeder. Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol 25, 859-867, 2018. PMCID6298426 PubMedPDF
390.A. Gaber, S.J. Kim, R.M. Kaake, M. Bencina, N. Krogan, A. Sali, M. Pavsic, B. Lenarcic. EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Sci Rep 8, 13269, 2018. PMCID6125409 PubMedPDF
389.M. Bonomi, S. Hanot, C.H. Greenberg, A. Sali, M. Nilges, M. Vendruscolo, R. Pellarin. Bayesian weighing of electron cryo-microscopy data for integrative structural modeling. Structure, pii: S0969-2126(18)30337-X, 2018. PMCID6779587 PubMedPDF bioRxiv
388.G.L. Holliday, E. Akiva, E.C. Meng, S.D. Brown, S. Calhoun, U. Pieper, A. Sali, S.J. Booker, P.C. Babbitt. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug & Play” Domain. Methods Enzymol 606, 1-71, 2018. PMCID6445391 PubMed
387.A. Lyon, A. Zelter, S. Viswanath, A. Maxwell, R. Johnson, K.C.B. Yabut, M. MacCoss, T.N. Davis, E. Muller, A. Sali, D.A. Agard. Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly. submitted. bioRxiv
386.J. Singla, K.M. McClary, K.L. White, F. Alber, A. Sali, R.C. Stevens. Opportunities and challenges in building a spatiotemporal multi-scale model of the human pancreatic β-cell. Cell 173, 11-19, 2018. PMCID6014618 PubMedPDF
385.B. Vallat, B. Webb, J. Westbrook, A. Sali, H.M. Berman. Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules. Structure 26, 894-904.e2, 2018. PMCID5990459 PubMedPDF
384.S.J. Kim, J. Fernandez-Martinez, I. Nudelman, Y. Shi, W. Zhang, B. Raveh, T. Herricks, B.D. Slaughter, J. Hogan, P. Upla, I.E. Chemmama, R. Pellarin, I. Echeverria, M. Shivaraju, A.S. Chaudhury, J. Wang, R. Williams, J.R. Unruh, C.H. Greenberg, E.Y. Jacobs, Z. Yu, M.J. de la Cruz, R. Mironska, D.L. Stokes, J.D. Aitchison, M.F. Jarrold, J.L. Gerton, S.J. Ludtke, C.W. Akey, B.T. Chait, A. Sali, M.P. Rout. Integrative Structure and Functional Anatomy of a Nuclear Pore Complex. Nature 555, 475-482, 2018. PMCID6022767 PubMedPDF
383.A.J. Guy, V. Irani, J.G. Beeson, B. Webb, A. Sali, J.S. Richards, P.A. Ramsland. Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. Sci Rep 8, 4355, 2018. PMCID5847524 PubMedPDF
382.S. Calhoun, M. Korczynska, D.J. Wichelecki, B. San Francisco, S. Zhao, D.A. Rodionov, M.W. Vetting, N.F. Al-Obaidi, H. Lin, M.J. O’Meara, D.A. Scott, J.H. Morris, D. Russel, S.C. Almo, A.L. Osterman, J.A. Gerlt, M.P. Jacobson, B.K. Shoichet, A. Sali. Prediction of enzymatic pathways by integrative pathway mapping. eLife 7, e31097, 2018. PMCID5788505 PubMedPDF
381.T. Yoshizawa, R. Ali, H.Y.J. Fung, K.A. Burke, Y. Lin, S.J. Kim, J. Jiou, M. Soniat, R. Oldenbourg, A. Sali, N.L. Fawzi, M.K. Rosen, Y.M. Chook. Nuclear import receptor inhibits phase separation of FUS through binding to multiple sites. Cell 173, 693-705, 2018. PMCID6234985 PubMedPDF
380.B. Webb, S. Viswanath, M. Bonomi, R. Pellarin, C.H. Greenberg, D. Saltzberg, A. Sali. Integrative structure modeling with the Integrative Modeling Platform. Prot Sci 27, 245-258, 2018. PMCID5734277 PubMedPDF
379.D. Schneidman-Duhovny, N. Khuri, G.Q. Dong, M.B. Winter, E. Shifrut, N. Friedman, C.S. Craik, K.P. Pratt, P. Paz, F. Aswad, A. Sali. Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PLoS ONE 13, e0206654, 2018. PMCID6219782 PubMedPDF bioRxiv
378.M.B. Winter, F. La Greca, S. Arastu-Kapur, P. Cimermancic, T.J. Buchholz, F. Caiazza, J.L. Anderl, M. Ravalin, M.F. Bohn, A. Sali, A.J. O’Donoghue, C.S. Craik. Immunoproteasome Functions Explained by Divergence in Cleavage Specificity and Regulation. eLife 6, e27364, 2017. PMCID5705213 PubMedPDF
377.S. Viswanath, I. Chemmama, P. Cimermancic, A. Sali. Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures. Biophys J 113, 2344-2353, 2017. PMCID5768525 PubMedPDF
376.S. Viswanath, M. Bonomi, S.J. Kim, V.A. Klenchin, K.C. Taylor, K.C. Yabut, N.T. Umbreit, H.A. Van Epps, J. Meehl, M.H. Jones, D. Russel, J.A. Velazquez-Muriel, M. Winey, I. Rayment, T.N. Davis, A. Sali, E.G. Muller. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol Biol Cell 28, 3298-3314, 2017. PMCID5687031 PubMedPDF
375.J. Trewhella, A.P Duff, D. Durand, F. Gabel, J.M. Guss, W.A. Hendrickson, G.L. Hura, D.A. Jacques, N.M. Kriby, A.H. Kwan, J. Perez, L. Pollack, T.M. Ryan, A. Sali, D. Schneidman-Duhovny, T. Schwede, D.I. Svergun, M. Sugiyama, J.A. Tainer, P. Vachette, J. Westbrook, A.E. Whitten. 2017 Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Cryst D D73, 710-728, 2017. PMCID5586245 PubMedPDF
374.S.K. Burley, G. Kurisu, J.L. Markley, H. Nakamura, S. Velankar, H.M. Berman, A. Sali, T. Schwede, J. Trewhella. PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models. Structure 25, 1317-1318, 2017. PMCID5821105 PubMedPDF
373.C.Y. Zhou, C.I. Stoddard, J.B. Johnston, M.J. Trnka, I. Echeverria, E. Palovcak, A. Sali, A.L. Burlingame, Y. Cheng, G.J. Narlikar. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep 19, 2033-2044, 2017. PMCID5564220 PubMedPDF
372.A. Stecula, A. Schlessinger, K. Giacomini, A. Sali. Human concentrative nucleoside transporter 3 (hCNT3, SLC28A3) forms a cyclic homotrimer. Biochemistry 56, 3475-3483, 2017. PMCID6917504 PubMedPDF
371.P.T. Manna, S. Obado, C. Boehm, C. Gadelha, G. van Miero, A. Sali, B. Chait, M. Rout, M.C. Field. Lineage-specific proteins essential for endocytosis in trypanosomes. J Cell Sci 130, 1379-1392, 2017. PMCID5399782 PubMedPDF
370.P. Upla, S.J. Kim, P. Sampathkumar, K. Dutta, S.M. Cahill, I.E. Chemmama, R. Williams, J.B. Bonanno, W.J. Rice, D.L. Stokes, D. Cowburn, S.C. Almo, A. Sali, M.P. Rout, J. Fernandez-Martinez. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure 25, 434-445, 2017. PMCID5342941 PubMedPDF
369.B. Webb, A. Sali. Protein structure modeling with MODELLER. In: Meth Mol Biol, 1654, pp. 39-54, 2017. PubMedPDF
368.E.C. Chen, N. Khuri, X. Liang, A. Stecula, H. Chien, S.W. Yee, Y. Huang, A. Sali, K.M. Giacomini. Discovery of competitive and non-competitive ligands of the organic cation transporter 1 (OCT1; SLC22A1). J Med Chem 60, 2685-2696, 2017. PubMedPDF
367.A. Chen, M. Vieth, D. Timm, C. Humblet, D. Schneidman-Duhovny, I.E. Chemmama, A. Sali, J. Lu, L. Liu. Reconstruction of 3D structures of MET Antibodies from Electron Microscopy 2D Class Averages. PloS One 12, e0175758, 2017. PMCID5391116 PubMedPDF
366.N. Khuri, A. Zur, M. Wittwer, L. Lin, S.W. Yee, A. Sali, K. Giacomini. Computational Discovery And Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1. J Chem Inf Model 57, 1402-1413, 2017. PubMedPDF
365.X. Wang, P. Cimermancic, C. Yu, A. Schweitzer, N. Chopra, J.L. Engel, C. Greenberg, A.S. Huszagh, F. Beck, E. Sakata, Y. Yang, E.J. Novitsky, A. Leitner, P. Nanni, A. Kahraman, X. Guo, J.E. Dixon, S.D. Rychnovsky, R. Aebersold, W. Baumeister, A. Sali, L. Huang. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics 16, 840-854, 2017. PMCID5417825 PubMedPDF
364.A. Jahangiri, S.W. Han, M.K. Sidorov, W. Chen, J. Rick, D. Schneidman-Duhovny, S. Mascharak, M. De Lay, J.R. Wagner, B. Imber, P.M. Flanigan, A. Chandra, R. Kuang, B.A. Castro, K. Lu, G. Bergers, A. Sali, W.A. Weiss, M.K. Aghi. Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer. Proc Natl Acad Sci USA 114, E8685-E8694, 2017. PMCID5642678 PubMedPDF
363.X. Wang, I.E. Chemmama, C. Yu, A. Huszagh, Y. Xu, R. Viner, S.A. Block, P. Cimermancic, S. Rychnovsky, Y. Ye, A. Sali, L. Huang. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J Biol Chem 292, 16310-16320, 2017. PMCID5625060 PubMedPDF
362.B. Webb, A. Sali. Comparative Protein Structure Modeling Using MODELLER. In: Curr Protoc Bioinformatics, 54, pp. 5.6.1-5.6.37, John Wiley and Sons, 2016. PMC5031415 PubMedPDF
361.C.H. Greenberg, J. Kollman, A. Zelter, R. Johnson, M.J. MacCoss, T.N. Davis, D.A. Agard, A. Sali. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol 194, 303-10, 2016. PMCID4866596 PubMedPDF
360.J. Fernandez-Martinez, S.J. Kim, Y. Shi, P. Upla, R. Pellarin, M. Gagnon, I.E. Chemmama, J. Wang, I. Nudelman, W. Zhang, R. Williams, W.J. Rice, D.L. Stokes, D. Zenklusen, B.T. Chait, A. Sali, M.P. Rout. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 167, 1215-1228, 2016. PMCID5130164 PubMedPDF
359.D.J. Saltzberg, H.B. Broughton, R. Pellarin, M.J. Chalmers, A. Espada, J.A. Dodge, B.D. Pascal, P.R. Griffin, C. Humblet, A. Sali. A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions. J Phys Chem B 121, 3493-3501, 2016. PMCID5693600 PubMedPDF
358.D.T. Barkan, X. Cheng, H. Celino, T. Tran, A. Bhandari, C.S. Craik, A. Sali, M.L. Smythe. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics 17, 481, 2016. PMCID5120537 PubMedPDF
357.B.L. Timney, B. Raveh, R. Mironska, J.M. Trivedi, S.J. Kim, D. Russel, S.R. Wente, A. Sali, M.P. Rout. Simple rules for passive diffusion through the nuclear pore complex. J Cell Biol 215, 57-76, 2016. PMCID5057280 PubMedPDF
356.U. Schulze-Gahmen, I. Echeverria, G. Stjepanovic, Y. Bai, H. Lu, D. Schneidman-Duhovny, J.A. Doudna, Q. Zhou, A. Sali, J.H. Hurley. Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife 5, e15910, 2016. PMCID5072841 PubMedPDF
355.J.C. Watts, K. Giles, D.J. Saltzberg, B.N. Dugger, S. Patel, A. Oehler, S. Bhardwaj, A. Sali, S.B. Prusiner. Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions. J Virol 90, 9558-9569, 2016. PMCID5068510 PubMedPDF
354.B. Webb, A. Sali. Comparative Protein Structure Modeling Using MODELLER. In: Curr Protoc Protein Sci, 86, pp. 2.9.1-2.9.37, John Wiley and Sons, 2016. PubMedPDF
353.Z.A. Chen, R. Pellarin, L. Fischer, A. Sali, M. Nilges, P.N. Barlow, J. Rappsilber. Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modelling. Mol Cell Proteomics 15, 2730-2743, 2016. PMCID4974347 PubMedPDF bioRxiv
352.D. Schneidman, M. Hammel, J. Tainer, A. Sali. FoXS, FoXSDock, and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res 44, W424-9, 2016. PMCID4987932 PubMedPDF
351.B. Raveh, J.M. Karp, S. Sparks, K. Dutta, M.P. Rout, A. Sali, D. Cowburn. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci USA 113, E2489-97, 2016. PMCID4983827 PubMedPDF
350.M.F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G.R. Lee, C. Seok, S. Qin, H. Zhou, D.W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, R.A.G. Chaleil, P.A. Bates, E. Ben-Zeev, M. Eisenstein, S.S. Negi, Z. Weng, T. Vreven, B.G. Pierce, T.M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J.P.G.L.M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A.S.J. Melquiond, K. Visscher, P.L. Kastritis, A.M.J.J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L.X. Peterson, H. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N.J. Bruce, J.C. Fuller, R.C. Wade, I. Anishchenko, P.J. Kundrotas, I.A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I.H. Moal, J. Férnandez-Recio, J.Y. Joung, J.Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D.R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C.A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S.S.R. Burman, J.J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, S.J. Wodak. Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins 84 Suppl 1, 323-48, 2016. PMCID5030136 PubMedPDF
349.J. Sprowl, S.S. Ong, A. Gibson, S. Hu, G. Du, W. Lin, L. Li, S. Bharill, R. Ness, A. Stecula, S. Offer, R. Diasio, A. Nies, M. Schwab, G. Cavaletti, E. Schlatter, G. Ciarimboli, J. Schellens, E. Isacoff, A. Sali, T. Chen, S. Baker, A. Sparreboom, N. Pabla. A phosphotyrosine switch regulates organic cation transporters. Nat Commun 7, 10880, 2016. PMCID4799362 PubMedPDF
348.P. Fromme, A. Sali. Editorial overview: Biophysical and molecular biological methods. Curr Opin Struct Biol 40, ix-xi, 2016. PubMedPDF
347.E. Lasater, E. Massi, A. Stecula, J. Politi, S. Tan, C. Smith, M. Gunthorpe, J. Holmes, F. Chehab, A. Sali, N. Shah. Novel TKI-resistant BCR-ABL1 Gatekeeper Residue Mutations Retain in vitro Sensitivity to Axitinib. Leukemia 30, 1405-9, 2016. PubMedPDF
346.P. Cimermancic, P. Weinkam, T.J. Rettenmaier, L. Bichmann, D.A. Keedy, R.A. Woldeyes, D. Schneidman-Duhovny, O.N. Demerdash, J.C. Mitchell, J.A. Wells, J.S. Fraser, A. Sali. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol 428, 709-19, 2016. PMCID4794384 PubMedPDF
345.J. LoPiccolo, S.J. Kim, Y. Shi, B. Wu, H. Wu, B.T. Chait, R.H. Singer, A. Sali, M. Brenowitz, A.R. Bresnick, J.M. Backer. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem 290, 30390-405, 2015. PMCID4683262 PubMedPDF
344.T. Rettenmaier, H. Fan, J. Karpiak, A. Doak, A. Sali, B. Shoichet, J. Wells. Small-molecule allosteric modulators of the protein kinase PDK1 from structure-based docking. J Med Chem 58, 8285-91, 2015. PMCID5099076 PubMedPDF
343.A.R. Choudhury, E. Sikorska, J. van den Boom, P. Bayer, L. Popenda, K. Szutkowski, S. Jurga, M. Bonomi, A. Sali, I. Zhukov, S. Passamonti, M. Novič. Structural model of the Bilitranslocase transmembrane domain supported by NMR and FRET data. PloS One 10, e0135455, 2015. PMCID4546402 PubMedPDF
342.C. Smith, K. Lin, A. Stecula, A. Sali, N. Shah. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia 29, 2390-2, 2015. PMCID4675689 PubMedPDF
341.R. Reid, M. Sgobba, B. Raveh, G. Rastelli, A. Sali, D. Santi. Analytical and simulation-based models for drug release and gel-degradation in a Tetra-PEG hydrogel drug-delivery system. Macromolecules 48, 7359-7369, 2015.PDF
340.P. Robinson, M. Trnka, R. Pellarin, C. Greenberg, D. Bushnell, R. Davis, A. Burlingame, A. Sali, R. Kornberg. Molecular architecture of the yeast Mediator complex. eLife 4, e08719, 2015. PMCID4631838 PubMedPDF
339.J. Luo, P. Cimermancic, S. Viswanath, C. Ebmeier, B. Kim, M. Dehecq, V. Raman, C. Greenberg, R. Pellarin, A. Sali, D. Taatjes, S. Hahn, J. Ranish. Architecture of the human and yeast general transcription and DNA repair factor TFIIH. Mol Cell 59, 794-806, 2015. PMCID4560838 PubMedPDF
338.Y. Shi, R. Pellarin, P. Fridy, J. Fernandez-Martinez, M. Thompson, Y. Li, Q.J. Wang, A. Sali, M. Rout, B. Chait. A strategy for dissecting the architectures of native macromolecular assemblies. Nat Methods 12, 1135-8, 2015. PMCID4803312 PubMedPDF
337.L. Carter, S.J. Kim, D. Schneidman-Duhovny, J. Stoehr, G. Poncet-Montange, T. Weiss, H. Tsuruta, S. Prusiner, A. Sali. Prion protein-antibody complexes characterized by chromatography-coupled small-angle X-ray scattering. Biophys J 109, 793-805, 2015. PMCID4547163 PubMedPDF
336.A. Sali, H. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S. Burley, J. Markley, H. Nakamura, P. Adams, A. Bonvin, W. Chiu, M. Dal Peraro, F. Di Maio, T. Ferrin, K. Grunewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C. Lawson, J. Meiler, M. Marti-Renom, G. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R. Read, H. Saibil, G. Schroder, C. Schwieters, C. Seidel, D. Svergun, M. Topf, E. Ulrich, S. Velanker, J. Westbrook. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23, 1156-67, 2015. PMCID4933300 PubMedPDF
335.J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. Prediction of functionally important phospho-regulatory events in Xenopus laevis oocytes. PLOS Comp Bio 11, e1004362, 2015. PMCID4552029 PubMedPDF
334.J. Kollman, C. Greenberg, S. Li, M. Moritz, A. Zelter, K. Fong, J. Fernandez, A. Sali, J. Kilmartin, T. Davis, D. Agard. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol 22, 132-137, 2015. PMCID4318760 PubMedPDF
333.A. Politis, C. Schmidt, E. Tjioe, A. Sandercock, K. Lasker, Y. Gordiyenko, D. Russel, A. Sali, C. Robinson. Topological models of heteromeric protein assemblies from mass spectrometry: Application to the yeast eIF3:eIF5 complex. Chem Biol 22, 117-128, 2015. PMCID4306531 PubMedPDF
332.E. Verschueren, J. Von Dollen, P. Cimermancic, N. Gulbahce, A. Sali, N. Krogan. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics 49, 8.19.1-8.19.16, 2015. PMCID4378866 PubMedPDF
331.B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. In: Curr Protoc Bioinformatics, 47, pp. 5.6.1-5.6.32, John Wiley and Sons, 2014. PubMedPDF
330.Y. Shi, J. Fernandez-Martinez, E. Tjioe, R. Pellarin, S.J. Kim, R. Williams, D. Schneidman, A. Sali, M. Rout, B. Chait. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics 13, 2927-2943, 2014. PMCID4223482 PubMedPDF
329.S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, A. Martel, T. Matsui, H. Tsuruta, T. Weiss, A. Markina-Inarrairaegui, J. Bonanno, M. Sauder, S. Burley, B.T. Chait, S. Almo, M. Rout, A. Sali. Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex. Mol Cell Proteomics 13, 2911-2926, 2014. PMCID4223481 PubMedPDF
328.M.H. Medema, P. Cimermancic, A. Sali, E. Takano, M. Fischbach. A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis. PLoS Comput Biol 10, e1004016, 2014. PMCID4256081 PubMedPDF
327.P. Cimermancic, M.H. Medema, J. Claesen, K. Kurita, L. Wieland Brown, K. Mavrommatis, A. Pati, P.A. Godfrey, M. Koehrsen, J. Clardy, B.W. Birren, E. Takano, A. Sali, R.G. Linington, M. Fischbach. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421, 2014. PMCID4123684 PubMedPDF
326.D. Schneidman-Duhovny, R. Pellarin, A. Sali. Uncertainty in Integrative Structural Modeling. Curr Opin Struct Biol 28, 96-104, 2014. PMCID4252396 PubMedPDF
325.J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex. Cell 158, 1125-1135, 2014. PMCID4151992 PubMedPDF
324.X. Zeng-Elmore, X. Gao, R. Pellarin, D. Schneidman-Duhovny, X. Zhang, K. Kozacka, Y. Tang, A. Sali, R. Chalkley, R. Cote, F. Chu. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol 426, 3713-3728, 2014. PMCID4253074 PubMedPDF
323.T. Street, X. Zeng, R. Pellarin, M. Bonomi, A. Sali, M. Kelly, F. Chu, D. Agard. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J Mol Biol 12, 2393-2404, 2014. PMCID5322795 PubMedPDF
322.R. Algret, J. Fernandez-Martinez, Y. Shi, S.J. Kim, R. Pellarin, P. Cimermancic, E. Cochet, A. Sali, B. Chait, M. Rout, S. Dokudovskaya. Molecular Architecture and Function of the SEA Complex  - a Modulator of the TORC1 Pathway. Mol Cell Proteomics 13, 2855-2870, 2014. PMCID4223477 PubMedPDF
321.G.Q. Dong, S. Calhoun, H. Fan, C. Kalyanaraman, N. London, M. Branch, S. Mashiyama, M. Jacobson, B. Shoichet, P. Babbitt, R. Armstrong, A. Sali. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 6, 1687-1699, 2014. PMCID4068255 PubMedPDF
320.Y. Spill, S.J. Kim, D. Schneidman-Duhovny, D. Russel, B. Webb, A. Sali, M. Nilges. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. J Synchrotron Radiat 21, 203-208, 2014. PMCID3874021 PubMedPDF
319.B. Webb, K. Lasker, J. Velazquez-Muriel, D. Schneidman-Duhovny, R. Pellarin, M. Bonomi, C. Greenberg, B. Raveh, E. Tjioe, D. Russel, A. Sali. Modeling of proteins and their assemblies with the Integrative Modeling Platform. In: Methods Mol Biol. Ed: Y. Chen, 1091, pp. 277-295, Humana Press, London, UK, 2014. PubMedPDF
318.K. Molnar, M. Bonomi, R. Pellarin, G. Clinthorne, G. Gonzalez, S. Goldberg, M. Goulian, A. Sali, W. DeGrado. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ. Structure 22, 1239-1251, 2014. PMCID4322757 PubMedPDF
317.U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 42, 336-346, 2014. PMCID3965011 PubMedPDF
316.M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. Determining protein complex structures based on a Bayesian model of in vivo FRET data. Mol Cell Proteomics 13, 2812-2823, 2014. PMCID4223474 PubMedPDF
315.B. Webb, A. Sali. Protein structure modeling with MODELLER. In: Methods in Molecular Biology. Ed: D. Kihara, 1137, pp. 1-15, Springer, New York, 2014.PDF
314.B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G.Q. Dong, A. Sali. Comparative Modeling of Drug Target Proteins. In: Chemistry, Molecular Sciences and Chemical Engineering. Ed: J. Reedijk, Elsevier, Waltham, MA, 2014.PDF
313.K. Berlin, C.A. Castaneda, D. Schneidman-Duhovny, A. Sali, A. Nava-Tudela, D. Fushman. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc 135, 16595-16609, 2013. PMCID3902174 PubMedPDF
312.C. Ryan, P. Cimermancic, Z. Szpiechy, A. Sali, R. Hernandez, N. Krogan. High-resolution network biology: connecting sequence with function. Nat Rev Genet 14, 865-879, 2013. PMCID4023809 PubMedPDF
311.A. Goble, R. Toro, X. Li, A. Ornelas, H. Fan, S. Eswaramoorthy, Y. Patskovsky, B. Hillerich, R. Seidel, A. Sali, B. Shoichet, S. Almo, S. Swaminathan, M. Tanner, F. Raushel. Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes. Biochemistry 52, 6525-6536, 2013. PMCID3813303 PubMedPDF
310.M. Kostic, C. Lima, A. Sali. Celebrating 20 Years of Structural Biology. Structure 21, 1477-1478, 2013. PMCID TBD by Journal. PubMedPDF
309.F. Martinez-Jimenez, G. Papadatos, L. Yang, I.M. Wallace, V. Kumar, U. Pieper, A. Sali, J.R. Brown, J.P. Overington, M.A. Marti-Renom. Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Comp Biol 9, e1003253, 2013. PMCID3789770 PubMedPDF
308.G.Q. Dong, H. Fan, D. Schneidman-Duhovny, B. Webb, A. Sali. Optimized atomic statistical potentials: Assessment of protein interfaces and loops. Bioinformatics 29, 3158-3166, 2013. PMCID3842762 PubMedPDF
307.P. Weinkam, A. Sali. Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations. J Phys Chem B 117, 13058-13068, 2013. PMCID3973026 PubMedPDF
306.C. Pandya, S. Brown, U. Pieper, A. Sali, D. Dunaway-Mariano, P. Babbitt, Y. Xia, K. Allen. The consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci USA 110, 3381-3387, 2013. PMCID3767544 PubMedPDF
305.D. Hitchcock, H. Fan, J. Kim, M. Vetting, B. Hillerich, R. Seidel, S. Almo, B. Shoichet, A. Sali, F. Raushel. Structure-guided Discovery of New Deaminase Enzymes. J Am Chem Soc 135, 13927-13933, 2013. PMCID38227683 PubMedPDF
304.D. Schneidman-Duhovny, M. Hammel, J. Tainer, A. Sali. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 105, 962-974, 2013. PMCID3752106 PubMedPDF
303.J. Trewhella, W. Hendrickson, G. Kleywegt, A. Sali, M. Sato, T. Schwede, D. Svergun, J. Tainer, J. Westbrook, H. Berman. Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB. Structure 21, 875-881, 2013. PMCID TBD by Journal PubMedPDF
302.A. Schlessinger, S.W. Yee, A. Sali, K. Giacomini. SLC classification: an update. Clin Pharmacol Ther 94, 19-23, 2013. PMCID4068830 PubMedPDF
301.E. Geier, A. Schlessinger, H. Fan, J. Gable, J. Irwin, A. Sali, K. Giacomini. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci USA 110, 5480-5485, 2013. PMCID3619328 PubMedPDF
300.A. Ward, A. Sali, I. Wilson. Integrative structural biology. Science 339, 913-915, 2013. PMCID3633482 PubMedPDF
299.P. Weinkam, Y.C. Chen, J. Pons, A. Sali. Impact of mutations on the allosteric conformational equilibrium. J Mol Biol 425, 647-661, 2013. PMCID3557769 PubMedPDF
298.M. Guttman, P. Weinkam, A. Sali, K. Lee. All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins. Structure 21, 321-331, 2013. PMCID3840220 PubMedPDF
297.A. Waight, B. Pedersen, A. Schlessinger, M. Bonomi, B. Chau, Z. Roe-Zurz, A. Risenmay, A. Sali, R. Stroud. Structural basis for alternating access of a Eukaryotic Calcium/Proton exchanger. Nature 499, 107-110, 2013. PMCID3702627 PubMedPDF
296.T. van Dam, M. Townsend, M. Turk, A. Schlessinger, A. Sali, M. Field, M. Huynen. Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proc Natl Acad Sci USA 110, 6943-6948, 2013. PMCID3637775 PubMedPDF
295.A. Schlessinger, N. Khuri, K. Giacomini, A. Sali. Molecular modeling and ligand docking for Solute Carrier (SLC) transporters. Curr Top Med Chem 13, 843-856, 2013. PMCID4056341 PubMedPDF
294.B. Pedersen, H. Kumar, A. Waight, A. Risenmay, Z. Roe-Zurz, B. Chau, A. Schlessinger, M. Bonomi, W. Harries, A. Sali, A. Johri, R. Stroud. Crystal structure of a eukaryotic phosphate transporter. Nature 496, 533-536, 2013. PMCID3678552 PubMedPDF
293.H. Gradisar, S. Bozic, T. Doles, D. Vengust, I. Hafner-Bratkovic, A. Mertelj, B. Webb, A. Sali, S. Klavzar, R. Jerala. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nat Chem Biol 9, 362-366, 2013. PMCID3661711 PubMedPDF
292.P. Sampathkumar, S.J. Kim, P. Upla, W. Rice, J. Phillips, B. Timney, U. Pieper, J. Bonanno, J. Fernandez-Martinez, Z. Hakhverdyan, N. Ketaren, T. Matsui, R. Weiss, D. Stokes, J.M. Sauder, S. Burley, A. Sali, M. Rout, S. Almo. Structure, dynamics, evolution and function of a major scaffold component in the Nuclear Pore Complex. Structure 21, 560-571, 2013. PMCID3755625 PubMedPDF
291.U. Pieper, A. Schlessinger, E. Kloppmann, G.A. Chang, J.J. Chou, M. Dumont, B. Fox, P. Fromme, W. Hendrickson, M. Malkowski, D. Rees, D. Stokes, M.H.B. Stowell, M. Wiener, B. Rost, R. Stroud, R. Stevens, A. Sali. Coordinating the impact of structural genomics on the human a-helical transmembrane proteome. Nat Struct Mol Biol 20, 135-138, 2013. PMCID3645303 PubMedPDF
290.M.B. Wittwer, A.A. Zur, N. Khuri, Y. Kido, A. Kosaka, X. Zhang, K.M. Morrissey, A. Sali, Y. Huang, K.M. Giacomini. Discovery of potent, selective multidrug and toxin extrusion Transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling. J Med Chem 56, 781-795, 2013. PMCID4068829 PubMedPDF
289.H. Fan, D. Hitchcock, R. Seidel, B. Hillerich, H. Lin, S. Almo, A. Sali, B. Shoichet, F. Raushel. The Assignment of Pterin Deaminase Activity to an Enzyme of Unknown Function Guided by Homology Modeling and Docking. J Am Chem Soc 135, 795-803, 2013. PMCID3557803 PubMedPDF
288.J.L. Markley, H. Akutsu, T. Asakura, M. Baldus, R. Boelens, A. Bonvin, R. Kaptein, A. Bax, I. Bezsonova, M.R. Gryk, J.C. Hoch, D.M. Korzhnev, M. Maciejewski, D. Case, W. Chazin, T. Cross, S. Dames, H. Kessler, O. Lange, T. Madl, B. Reif, M. Sattler, D. Eliezer, A. Fersht, J. Forman-Kay, L. Kay, J. Fraser, J. Gross, T. Kortemme, A. Sali, T. Fujiwara, K. Gardner, X. Luo, J. Rizo-Rey, M. Rosen, R. Gil, C. HO, G. Rule, A. Gronenborn, R. Ishima, J. Klein-Seetharaman, P. Tang, P. van der Wel, Y. Xu, S. Grzesiek, S. Hiller, J. Seelig, E. Laue, H. Mott, D. Nietlispach, I. Barsukiv, L. Lian, D. Middleton, T. Blumenschein, G. Moore, I. Campbell, J. Schnell, I. Vakonakis, A. Watts, M. Conte, J. Mason, M. Pfuhl, M. Sanderson, J. Craven, M. Williamson, C. Dominguez, G. Roberts, U. Gunther, M. Overduin, J. Werner, P. Williamson, C. Blindauer, M. Crump, P. Driscoll, T. Frenkiel, A. Golovanov, S. Matthews, J. Parkinson, D. Uhrin, M. Williams, D. Neuhaus, H. Oschkinat, A. Ramos, D. Shaw, C. Steinbeck, M. Vendruscolo, G. Vuister, K. Walters, H. Weinstein, K. Wuthrich, S. Yodoyama. In support of the BMRB. Nat Struct Mol Biol 19, 854-860, 2012. PMCID TBD by Journal PubMedPDF
287.D. Schneidman-Duhovny, S.J. Kim, A. Sali. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12, 17, 2012. PMCID3427135 PubMedPDF
286.A. Schlessinger, M.B. Wittwer, A. Dahlin, N. Khuri, M. Bonomi, H. Fan, K. Giacomini, A. Sali. High Selectivity of the γ-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach. J Biol Chem 287, 37745-37756, 2012. PMCID3488050 PubMedPDF
285.P. Kolb, K. Phan, Z. Gao, A. Marko, A. Sali, K.A. Jacobson. Limits of ligand selectivity from docking to models: In silico screening for A1 adenosine receptor antagonists. PLoS One 7, e49910, 2012. PMCID3503826 PubMedPDF
284.J.A. Velazquez-Muriel, K. Lasker, D. Russel, J. Phillips, B. Webb, D. Schneidman-Duhovny, A. Sali. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proc Natl Acad Sci USA 109, 18821-18826, 2012. PMCID3503186 PubMedPDF
283.O. Martinez-Avila, S. Wu, S.J. Kim, Y. Cheng, F. Khan, R. Samudrala, A. Sali, J. Horst, S. Habelitz. Self-assembly of Filamentous Amelogenin Requires Calcium and Phosphate: From Dimers via Nanoribbons to Fibrils. Biomacromolecules 13, 3494-3502, 2012. PMCID3496023 PubMedPDF
282.J. Trinidad, D. Barkan, B. Gulledge, A. Thalhammer, A. Sali, R. Schoepfer, A. Burlingame. Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse. Mol Cell Proteomics 11, 215-229, 2012. PMCID3412957 PubMedPDF
281.J.A. Horst, U. Pieper, A. Sali, L. Zhan, G. Chopra, R. Samudrala, J.D.B. Featherstone. Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res 22, 86-93, 2012. PMCID3420364 PubMedPDF
280.H. Braberg, B. Webb, E. Tjioe, U. Pieper, A. Sali, M.S. Madhusudhan. SALIGN: A webserver for alignment of multiple protein sequences and structures. Bioinformatics 15, 2072-2073, 2012. PMCID3400954 PubMedPDF
279.A. Morin, J. Urban, P.D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz. Shining Light into Black Boxes. Science 336, 159-160, 2012. PMCID4203337 PubMedPDF
278.V. Puizdar, T. Zajc, E. Zerovnik, M. Renko, U. Pieper, N. Eswar, A. Sali, I. Dolenc, V. Turk. Biochemical Characterization and Structural Modeling of Human Cathepsin E Variant 2 in Comparison to the Wild-type Protein. Biol Chem 393, 177-186, 2012. PMCID4111641 PubMedPDF
277.D. Schneidman-Duhovny, A. Rossi, A. Avila-Sakar, S.J. Kim, J. Velazquez-Muriel, P. Strop, H. Liang, K.A. Krukenberg, M. Liao, H.M. Kim, S. Sobhanifar, V. Dotsch, A. Raipal, J. Pons, D.A. Agard, Y. Cheng, A. Sali. A Method for Integrative Structure Determination of Protein-Protein Complexes. Bioinformatics 28, 3282-3289, 2012. PMCID3519461 PubMedPDF
276.C. Klammt, I. Maslennikov, M. Bayrhuber, C. Eichmann, N. Vajpai, E. Chiu, K. Blain, L. Esquivies, H. Kwon, B. Balana, U. Pieper, A. Sali, P. Slesinger, W. Kwiatkowski, R. Rick, S. Choe. Facile Backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods 8, 834-839, 2012. PMCID3723349 PubMedPDF
275.P. Sampathkumar, S.J. Kim, D. Manglicmot, K.T. Bain, J. Gilmore, T. Gheyi, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, T. Matsui, H. Tsuruta, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, M. Rout, A. Sali, J.M. Sauder, S.C. Almo, S.K. Burley. Atomic structure of the Nuclear Pore Complex targeting domain of Nup116 homologue from the yeast, Candida glabrata. Proteins:Struct Funct Bioinform 8, 2110-2116, 2012. PMCID3686472 PubMedPDF
274.K. Lasker, F. Forster, S. Bohn, T. Walzthoeni, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, W. Baumeister. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109, 1380-1387, 2012. PMCID3277140 PubMedPDF
273.G. Pathare, I. Nagy, S. Bohn, P. Unverdorben, A. Hubert, R. Korner, S. Nickell, K. Lasker, A. Sali, T. Tamura, T. Nishioka, F. Forster, W. Baumeister, A. Bracher. The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together. Proc Natl Acad Sci USA 109, 149-154, 2012. PMCID3252951 PubMedPDF
272.D. Russel, K. Lasker, B. Webb, J. Velazquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, A. Sali. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol 10, e1001244, 2012. PMCID3260315 PubMedPDF
271.P. Weinkam, J. Pons, A. Sali. Structure-based Model of Allostery Predicts Coupling Between Distant Sites. Proc Natl Acad Sci USA 109, 4875-4880, 2012. PMCID3324024 PubMedPDF
270.R. Henderson, A. Sali, M. Baker, B. Carragher, B. Devkota, K. Downing, E. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. Ludtke, O. Medalia, P. Penczek, P. Rosenthal, M. Rossmann, M. Schmid, G. Schroder, A. Steven, D. Stokes, J. Westbrook, W. Wriggers, H. Yang, J. Young, H. Berman, W. Chiu, G. Kleywegt, C. Lawson. Outcome of the First Electron Microscopy Validation Task Force Meeting. Structure 20, 205-214, 2012. PMCID3328769 PubMedPDF
269.J. Fernandez-Martinez, J. Phillips, M. Sekedat, R. Diaz-Avalos, J. Velazquez-Muriel, J. Franke, R. Williams, D. Stokes, B. Chait, A. Sali, M. Rout. Structure-function Map for a Heptameric Component of the Nuclear Pore Complex. J Cell Biol 196, 419-434, 2012. PMCID3283990 PubMedPDF
268.H. Fan, J. Irwin, A. Sali. Virtual Ligand Screening Against Comparative Protein Structure Models. Methods Mol Biol 819, 105-126, 2012. PMCID3386294 PubMedPDF
267.K. Lasker, J. Velazquez-Muriel, B. Webb, Z. Yang, T.E. Ferrin, A. Sali. Macromolecular assembly structures by comparative modeling and electron microscopy. In: Methods in Molecular Biology. Ed: J. Walker, pp. 331-350, Humana Press, New York, NY, 2012. PMCID TBD by Journal. PubMedPDF
266.Z. Yang, K. Lasker, D. Schneidman-Duhovny, B. Webb, C. Huang, E. Pettersen, T. Goddard, E. Meng, A. Sali, T. Ferrin. UCSF Chimera, MODELLER, and IMP: an integrated Modeling System. J Struct Biol 179, 269-278, 2012. PMCID3410985 PubMedPDF
265.J. Gerlt, K. Allen, S. Almo, R. Armstrong, P. Babbitt, J. Cronan, D. Dunaway-Mariano, H. Imker, M. Jacobson, W. Minor, C. Poulter, F. Raushel, A. Sali, B. Shoichet, J. Sweedler. The Enzyme Function Initiative. Biochemistry 50, 9950-9962, 2011. PMCID3238057 PubMedPDF
264.A.M. Goble, H. Fan, A. Sali, F.M. Raushel. Discovery of a Cytokinin Deaminase. ACS Chem Biol 6, 1036-1040, 2011. PMCID3199332 PubMedPDF
263.J. Choi, S. Yee, A. Ramirez, K. Morrissey, G. Jang, P. Joski, J. Mefford, S. Hesselson, A. Schlessinger, G. Jenkins, R. Castro, S. Johns, D. Stryke, A. Sali, T. Ferrin, J. Witte, P. Kwok, D. Roden, R. Wilke, C. McCarty, R. Davis, K. Giacomini. A Common Promoter Variant in MATE2-K Is Associated with Poor Response to Metformin. Clin Pharmacol Ther 90, 674-684, 2011. PMCID3329222 PubMedPDF
262.A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali. Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET. Proc Natl Acad Sci USA 108, 15810-15815, 2011. PMCID3179104 PubMedPDF
261.J. Carlsson, R. Coleman, V. Setola, J. Irwin, H. Fan, A. Schlessinger, A. Sali, B. Roth, B. Shoichet. Structure-based Ligand Discovery Against a Homology Model and X-ray Structure of the Dopamine D3 Receptor. Nat Chem Biol 7, 769-778, 2011. PMCID3197762 PubMedPDF
260.E. Tjioe, K. Lasker, B. Webb, H. Wolfson, A. Sali. MultiFit: A web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res 39, 167-170, 2011. PMCID3125811 PubMedPDF
259.S. Jager, D.Y. Kim, K. Shindo, E. Kwon, R. LaRue, C. Mahon, P. Cimermancic, L. Yen, D. Stanley, M. Li, A. Burlingame, A. Sali, C. Craik, R. Harris, J. Gross, N. Krogan. Vif Hijacks CBFβ to Degrade APOBEC3G and Promote HIV-1 Infection. Nature 481, 371-375, 2011. PMCID3310910 PubMedPDF
258.S. Jager, P. Cimermancic, N. Gulbahce, J. Johnson, K. McGovern, S. Clarke, M. Shales, G. Mercenne, K. Li, H. Barry, G. Jang, E. Akiva, L. Pache, J. Marlett, S. Roth, M. Stephens, I. D’Orso, J. Fernandes, M. Fahey, C. Mahon, A. O’Donoghue, A. Todorovic, J. Morris, D. Maltby, T. Alber, G. Cagney, F. Bushman, J. Young, S. Chanda, W. Sundquist, T. Kortemme, R. Hernandez, C. Craik, A. Burlingame, A. Sali, A. Frankel, N. Krogan. Global Landscape of HIV-Human Protein Complexes. Nature 481, 365-370, 2011. PMCID3310911 PubMedPDF
257.H. Fan, D. Schneidman, J.J. Irwin, G. Dong, B. Shoichet, A. Sali. Statistical Potential for Modeling and Ranking Protein-Ligand Interactions. J Chem Inf Model 51, 3078-3092, 2011. PMCID3246566 PubMedPDF
256.M. Field, A. Sali, M. Rout. On a bender: Bars, ESCRTs, COPs, and finally getting your coat. J Cell Biol 193, 963-972, 2011. PMCID3115789 PubMedPDF
255.S. Dokudovskaya, F. Waharte, A. Schlessinger, U. Pieper, D.P. Devos, I.M. Cristea, R. Williams, J. Salamero, B.T. Chait, A. Sali, M.C. Field, M.C. Rout, C. Dargemont. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics 10, M110.006478, 2011. PMCID3108837 PubMedPDF
254.S.S. Kamat, H. Fan, J.M. Sauder, S.K. Burley, B.K. Shoichet, A. Sali, F.M. Raushel. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc 133, 2080-2083, 2011. PMCID3043370 PubMedPDF
253.P. Sampathkumar, T. Gheyi, S.A. Miller, K.T. Bain, M. Dickey, J.B. Bonanno, Kim. S.J., J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, A. Sali, J.M. Sauder, S.K. Burley. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the Nuclear Pore Complex. Proteins:Struct Funct Bioinform 79, 1672-1677, 2011. PMCID3350809 PubMedPDF
252.B. Webb, K. Lasker, D. Schneidman-Duhovny, E. Tjioe, J. Phillips, S.J. Kim, J. Velazquez-Muriel, D. Russel, A. Sali. Modeling of Proteins and their Assemblies with the Integrative Modeling Platform. In: Methods in Molecular Biology, pp. 377-397, Humana Press, 2011. PMCID TBD by Journal. PubMedPDF
251.S.S. Kamat, A. Bagaria, D. Kumaran, G.P. Holmes-Hampton, H. Fan, A. Sali, J.M. Sauder, S.K. Burley, P.A. Lindahl, S. Swaminathan, F.M. Raushel. Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase. Biochemistry 50, 1917-1927, 2011. PMCID3059353 PubMedPDF
250.U. Pieper, B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E.C. Meng, E.F. Pettersen, C.C. Huang, R.S. Datta, P. Sampathkumar, M.S. Madhusudhan, K. Sjolander, T.E. Ferrin, S.K. Burley, A. Sali. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 39, 465-474, 2011. PMCID3013688 PubMedPDF
249.L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. Response to "Predictable difficulty or difficulty to predict" by Tamas Aranyi, Krisztina Fulop, Orsolya Symmons, Viola Pomozi, and Andras Varadi. Protein Sci 20, 4-5, 2011.PDF
248.D. Schneidman-Duhovny, M. Hammel, A. Sali. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol 3, 461-471, 2011. PMCID3040266 PubMedPDF
247.F. Forster, K. Lasker, S. Nickell, A. Sali, W. Baumeister. Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics 9, 1666-1677, 2010. PMCID2938054 PubMedPDF
246.L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. Functional Hot Spots in Human ATP-binding Cassette Transporter Nucleotide Binding Domains. Protein Sci 19, 2110-2121, 2010. PMCID3005782 PubMedPDF
245.L. Chen, M. Takizawa, E. Chen, A. Schlessinger, J.H. Choi, J. Segenthelar, A. Sali, M. Kubo, S. Nakamura, Y. Iwamoto, N. Iwasaki, K.M. Giacomini. Genetic polymorphisms in the organic cation transporter 1, OCT1, in Chinese and Japanese populations, exhibit altered function. J Pharmacol Exp Ther 1, 42-50, 2010. PMCID2957788 PubMedPDF
244.K. Lasker, A. Sali, H.J. Wolfson. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins:Struct Funct Bioinform 78, 3205-3211, 2010. PMCID2952722 PubMedPDF
243.P. Sampathkumar, F. Lu, X. Zhao, Z. Li, J. Gilmore, K. Bain, M.E. Rutter, T. Gheyi, K. Schwinn, J. Bonanno, U. Pieper, J.E. Fajardo, A. Fiser, S. Almo, A. Swaminathan, M. Chance, D. Baker, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, A. Sali, J.M. Sauder, S. Burley. Structure of a putative BenF-like porin from Pseudomanas fluorescens Pf-5 at 2.6 Å resolution. Proteins:Struct Funct Bioinform 78, 3056-3062, 2010. PMCID2989796 PubMedPDF
242.P. Sampathkumar, S.A. Ozyurt, J. Do, K.T. Bain, M. Dickey, L.A. Rodgers, T. Gheyi, A. Sali, S.J. Kim, J. Phillips, U. Pieper, J. Fernandez-Martinez, J.D. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, J.M. Sauder, S.K. Burley. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup 145. Proteins:Struct Funct Bioinform 78, 1992-1998, 2010. PMCID3136511 PubMedPDF
241.K. Lasker, J.L. Phillips, D. Russel, J. Velazquez-Muriel, D. Schneidman-Duhovny, B. Webb, A. Schlessinger, A. Sali. Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data. Mol Cell Proteomics 9, 1689-1702, 2010. PMCID2938050 PubMedPDF
240.D. Schneidman-Duhovny, M. Hammel, A. Sali. FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles. Nucleic Acids Res 38, 541-544, 2010. PMCID2896111 PubMedPDF
239.A. Schlessinger, P. Matsson, J.E. Shima, U. Pieper, S.W. Yee, L. Kelly, L. Apeltsin, R.M. Stroud, T.E. Ferrin, K.M. Giacomini, A. Sali. Comparison of Human Solute Carriers. Protein Sci 19, 412-428, 2010. PMCID2866268 PubMedPDF
238.L. Chen, B. Pawlikowski, A. Schlessinger, S. More, D. Stryke, S.J. Johns, M. Portman, T.E. Ferrin, A. Sali, K. Giacomini. Role of organic cation transporter 3 (SLC22A3) and Its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics 20, 687-699, 2010. PMCID2976715 PubMedPDF
237.F. Gruswitz, S. Chaudhary, J. Ho, A. Schlessinger, P. Bobak, C. Ho, A. Sali, C. Westhoff, R. Stroud. Function of Human Rh based on Structure of RhCG at 2.1 Å. Proc Natl Acad Sci U S A 107, 9638-9643, 2010. PMCID2906887 PubMedPDF
236.D. Barkan, D. Hostetter, S. Mahrus, U. Pieper, J. Wells, C. Craik, A. Sali. Prediction of Protease Substrates using Sequence and Structure Features. Bioinformatics 26, 1714-1722, 2010. PMCID2894511 PubMedPDF
235.F.P. Davis, A. Sali. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comp Biol 6, e1000668, 2010. PMCID2816688 PubMedPDF
234.D. Kroetz, N. Ahituv, E. Burchard, S. Guo, A. Sali, K. Giacomini. The Pharmacogenomics Center of the University of California, Sam Francisco: At the interface of genomics, biological mechanism and drug therapy. Pharmacogenomics 10, 1569-1576, 2009. PMCID2923222 PubMedPDF
233.F. Forster, K. Lasker, F. Beck, S. Nickell, A. Sali, W. Baumeister. An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem Biophys Res Commun 388, 228-233, 2009. PMCID2771176 PubMedPDF
232.H. Fan, J.J. Irwin, B.M. Webb, G. Klebe, B. Shoichet, A. Sali. Molecular Docking Screens Using Comparative Models of Proteins. J Chem Inf Model 49, 2512-2527, 2009. PMCID2790034 PubMedPDF
231.D.J. Taylor, B. Devkota, A.D. Huang, M. Topf, N. Eswar, A. Sali, S.C. Harvey, J. Frank. Comprehensive Molecular Structure of the Eukaryotic Ribosome. Structure 17, 1591-1604, 2009. PMCID2814252 PubMedPDF
230.T. Lezon, A. Sali, I. Bahar. Global motions of the nuclear pore complex:Insights from Elastic Network Models. PLoS Comp Biol 5, e1000496, 2009. PMCID2725293 PubMedPDF
229.L. Kelly, U. Pieper, N. Eswar, F.A. Hays, M. Li, Z. Roe-Zurz, D. Kroetz, K.M. Giacomini, R.M. Stroud, A. Sali. A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics 10, 269-280, 2009. PMCID2780624 PubMedPDF
228.J.A. DeGrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, B.T. Chait. The Establishment of Nuclear Pore Complex Architecture Occurred Early in Evolution. Mol Cell Proteomics 8, 2119-2130, 2009. PMCID2742445 PubMedPDF
227.M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, A. Sali. Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel 22, 569-574, 2009. PMCID2909824 PubMedPDF
226.K. Lasker, M. Topf, A. Sali, H.J. Wolfson. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J Mol Biol 388, 180-194, 2009. PMCID2680734 PubMedPDF
225.S. Nickell, F. Beck, S.H.W. Scheres, A. Korinek, F. Forster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, A. Sali, J. Plitzko, J.-M. Carazo, M. Mann, W. Baumeister. Insights into the Molecular Architecture of the 26S Proteasome. Proc Natl Acad Sci U S A 29, 11943-11947, 2009. PMCID2715492 PubMedPDF
224.O. Fornes, R. Aragues, J. Espadaler, M.A. Marti-Renom, A. Sali, B. Oliva. ModLink+: Improving fold recognition by using protein-protein interactions. Bioinformatics 25, 1506-1512, 2009. PMCID2687990 PubMedPDF
223.L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. A kernel for the Tropical Disease Initiative. Nat Biotechnol 27, 320-321, 2009. PMCID3088649 PubMedPDF
222.R.M. Stroud, S. Choe, J. Holton, H.R. Kaback, W. Kwiatkowski, D.L. Minor, R. Riek, A. Sali, H. Stahlberg, W. Harries. 2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins. J Struct Funct Genom 10, 193-208, 2009. PMCID2705707 PubMedPDF
221.K.C. Pandey, D.T. Barkan, A. Sali, P.J. Rosenthal. Regulatory elements within the prodomain of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. PLoS One 4(5):e5694, 2009. PMCID2682653 PubMedPDF
220.L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis 3, e418, 2009. PMCID2667270 PubMedPDF
219.T. Schwede, A. Sali, B. Honig, M. Levitt, H.M. Berman, D. Jones, S.E. Brenner, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack Jr, K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R. Krystek Jr, T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, I.A. Wilson. Outcome of a workshop on applications of protein models in biomedical research. Structure 17, 151-159, 2009. PMCID2739730 PubMedPDF
218.D. Russel, K. Lasker, J. Phillips, D. Schneidman-Duhovny, J.A. Velazquez-Muriel, A. Sali. The structural dynamics of macromolecular processes. Curr Opin Cell Biol 21, 97-108, 2009. PMCID2774249 PubMedPDF
217.M.E. Peterson, F. Chen, J.G. Saven, D.S. Roos, P.C. Babbitt, A. Sali. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci 18, 1306-1315, 2009. PMCID2774440 PubMedPDF
216.M. Li, F.A. Hays, Z. Roe-Zurz, L. Vuong, L. Kelly, C.M. Ho, R.M. Robbins, U. Pieper, J.D. O'Connell 3rd, L.J. Miercke, K.M. Giacomini, A. Sali, R.M. Stroud. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol 385, 820-830, 2009. PMCID2659619 PubMedPDF
215.F.A. Hays, Z. Roe-Zurz, M. Li, L. Kelly, F. Gruswitz, A. Sali, R.M. Stroud. Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. J Struct Funct Genom 10, 9-16, 2009. PMCID2756966 PubMedPDF
214.U. Pieper, N. Eswar, B.M. Webb, D. Eramian, L. Kelly, D.T. Barkan, H. Carter, P. Mankoo, R. Karchin, M.A. Marti-Renom, F.P. Davis, A. Sali. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 37, D347-354, 2009. PMCID2686492 PubMedPDF
213.U. Pieper, R. Chiang, J.J. Seffernick, S.D. Brown, M.E. Glasner, L. Kelly, N. Eswar, J.M. Sauder, J.B. Bonanno, S. Swaminathan, S.K. Burley, X. Zheng, M.R. Chance, S.C. Almo, J.A. Gerlt, F.M. Raushel, M.P. Jacobson, P.C. Babbitt, A. Sali. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genom 10, 107-125, 2009. PMCID2693957 PubMedPDF
212.N. Eswar, A. Sali. Protein Structure Modeling. In: From Molecules to Medicine, Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism. Ed: J.L. Sussman, P. Spadon, pp. 139-151, Springer-Verlag, Dordrecht, The Netherlands, 2009.PDF
211.S. Graslund, P. Nordlund, J. Weigelt, B.M. Hallberg, J. Bray, O. Gileadi, S. Knapp, U. Oppermann, C. Arrowsmith, R. Hui, J. Ming, S. dhe-Paganon, H. Park, A. Savchenko, A. Yee, A. Edwards, R. Vincentelli, C. Cambillau, R. Kim, S. Kim, Z. Rao, Y. Shi, T.C. Terwilliger, C. Kim, L. Hung, G.S. Waldo, Y. Peleg, S. Albeck, T. Unger, O. Dym, J. Prilusky, J.L. Sussman, R.C. Stevens, S.A. Lesley, I.A. Wilson, A. Joachimiak, F. Collart, I. Dementieva, M.I. Donnelly, W.H. Eschenfeldt, Y. Kim, L. Stols, R. Wu, M. Zhou, S.K. Burley, J.S. Emtage, J.M. Sauder, D. Thompson, K. Bain, J. Luz, T. Gheyi, F. Zhang, S. Atwell, S.C. Almo, J.B. Bonanno, A. Fiser, S. Swaminathan, F.W. Studier, M.R. Chance, A. Sali, T.B. Acton, R. Xiao, L. Zhao, L.C. Ma, J.F. Hunt, L. Tong, K. Cunningham, M. Inouye, S. Anderson, H. Janjua, R. Shastry, C.K. Ho, D. Wang, H. Wang, M. Jiang, G.T. Montelione, D.I. Stuart, R.J. Owens, S. Daenke, A. Schutz, U. Heinemann, S. Yokoyama, K. Bussow, K.C. Gunsalus. Protein production and purification (vol 5, pg 135, 2008). Nat Methods 5, 369-369, 2008. PMCID3178102 PubMedPDF
210.I.I. Serysheva, S.J. Ludtke, M.L. Baker, Y. Cong, M. Topf, D. Eramian, A. Sali, S.L. Hamilton, W. Chiu. Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A 105, 9610-9615, 2008. PMCID2474495 PubMedPDF
209.S. Mahrus, J.C. Trinidad, D.T. Barkan, A. Sali, A.L. Burlingame, J.A. Wells. Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini. Cell 134, 866-876, 2008. PMCID2566540 PubMedPDF
208.R.A. Chiang, A. Sali, P.C. Babbitt. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 4, e1000142, 2008. PMCID2453236 PubMedPDF
207.C.M. Anderson, D. Korkin, D.L. Smith, S. Makovets, J.J. Seidel, A. Sali, E.H. Blackburn. Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break. Genes Dev 22, 854-859, 2008. PMCID2279195 PubMedPDF
206.F. Forster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali. Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol 382, 1089-1106, 2008. PMCID2745287 PubMedPDF
205.D. Eramian, N. Eswar, M.Y. Shen, A. Sali. How well can the accuracy of comparative protein structure models be predicted? Protein Sci 17, 1881-1893, 2008. PMCID2578807 PubMedPDF
204.K.A. Krukenberg, F. Forster, L.M. Rice, A. Sali, D.A. Agard. Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure 16, 755-765, 2008. PMCID2600884 PubMedPDF
203.R. Karchin, M. Agarwal, A. Sali, F. Couch, M.S. Beattie. Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios. Cancer Inform 6, 203-216, 2008. PMCID2587343 PubMedPDF
202.F. Aguero, B. Al-Lazikani, M. Aslett, M. Berriman, F.S. Buckner, R.K. Campbell, S. Carmona, I.M. Carruthers, A.W. Chan, F. Chen, G.J. Crowther, M.A. Doyle, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, J.P. Overington, A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. Van Voorhis, C.L. Verlinde. Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov 7, 900-907, 2008. PMCID3184002 PubMedPDF
201.J. Espadaler, N. Eswar, E. Querol, F.X. Aviles, A. Sali, M.A. Marti-Renom, B. Oliva. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics 9, 249, 2008. PMCID2430716 PubMedPDF
200.M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali. Protein structure fitting and refinement guided by cryo-EM density. Structure 16, 295-307, 2008. PMCID2409374 PubMedPDF
199.F. Alber, F. Forster, D. Korkin, M. Topf, A. Sali. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77, 443-477, 2008. PubMedPDF
198.P. Chandramouli, M. Topf, J.F. Menetret, N. Eswar, J.J. Cannone, R.R. Gutell, A. Sali, C.W. Akey. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure 16, 535-548, 2008. PMCID2775484 PubMedPDF
197.F. Alber, B.T. Chait, M.P. Rout, A. Sali. Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints. In: Protein-protein interactions and networks: identification, characterization and prediction. Ed: A. Panchenko, T. Przytycka, pp. 99-114, Springer-Verlag, London, UK, 2008.PDF
196.S.K. Burley, S.C. Almo, J.B. Bonanno, M.R. Chance, S. Emtage, A. Fiser, A. Sali, J.M. Sauder, S. Swaminathan. Structure Genomics of Protein Superfamilies. In: Structural Bioinformatics, 2nd Edition. Ed: J. Gu, P.E. Bourne, Wiley-Blackwell, New York, NY, 2008.
195.C.R. Booth, A.S. Meyer, Y. Cong, M. Topf, A. Sali, S.J. Ludtke, W. Chiu, J. Frydman. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol 15, 746-753, 2008. PMCID2546500 PubMedPDF
194.Y. Cong, M. Topf, A. Sali, P. Matsudaira, M. Dougherty, W. Chiu, M.F. Schmid. Crystallographic conformers of actin in a biologically active bundle of filaments. J Mol Biol 375, 331-336, 2008. PMCID2680129 PubMedPDF
193.T. Schwede, A. Sali, N. Eswar, M.C. Peitsch. Protein Structure Modeling. In: Computational Structural Biology. Ed: T. Schwede, M.C. Peitsch, pp. 3-35, World Scientific Publishing Ltd., Singapore, 2008.PDF
192.N. Eswar, D. Eramian, B. Webb, M.Y. Shen, A. Sali. Protein structure modeling with MODELLER. Methods Mol Biol 426, 145-159, 2008. PubMedPDF
191.F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, M.P. Rout, A. Sali. Determining the architectures of macromolecular assemblies. Nature 450, 683-694, 2007. PubMedPDF
190.F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, A. Sali, M.P. Rout. The molecular architecture of the nuclear pore complex. Nature 450, 695-701, 2007. PubMedPDF
189.C.V. Robinson, A. Sali, W. Baumeister. The molecular sociology of the cell. Nature 450, 973-982, 2007. PubMedPDF
188.V.D. Winn, R. Haimov-Kochman, A.C. Paquet, Y.J. Yang, M.S. Madhusudhan, M. Gormley, K.T. Feng, D.A. Bernlohr, S. McDonagh, L. Pereira, A. Sali, S.J. Fisher. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology 148, 1059-1079, 2007. PubMedPDF
187.A. Sali, C.D. Lima, M. Kostic. Structural genomics. Structure 15, 1341, 2007. PubMedPDF
186.F. Melo, A. Sali. Fold assessment for comparative protein structure modeling. Protein Sci 16, 2412-2426, 2007. PubMedPDF
185.S.C. Almo, J.B. Bonanno, J.M. Sauder, S. Emtage, T.P. Dilorenzo, V. Malashkevich, S.R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U.A. Ramagopal, J. Faber-Barata, M.R. Chance, A. Sali, A. Fiser, Z.Y. Zhang, D.S. Lawrence, S.K. Burley. Structural genomics of protein phosphatases. J Struct Funct Genom 8, 121-140, 2007. PubMedPDF
184.F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, A. Sali. Host pathogen protein interactions predicted by comparative modeling. Protein Sci 16, 2585-2596, 2007. PubMedPDF
183.M.A. Marti-Renom, U. Pieper, M.S. Madhusudhan, A. Rossi, N. Eswar, F.P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali. DBAli tools: mining the protein structure space. Nucleic Acids Res 35, W393-397, 2007. PubMedPDF
182.M.A. Marti-Renom, A. Rossi, F. Al-Shahrour, F.P. Davis, U. Pieper, J. Dopazo, A. Sali. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics 8 Suppl 4, S4, 2007. PubMedPDF
181.R. Aragues, A. Sali, J. Bonet, M.A. Marti-Renom, B. Oliva. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol 3, 1761-1771, 2007. PubMedPDF
180.K. Bajaj, M.S. Madhusudhan, B.V. Adkar, P. Chakrabarti, C. Ramakrishnan, A. Sali, R. Varadarajan. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol 3, e241, 2007. PubMedPDF
179.N. Soranzo, L. Kelly, L. Martinian, M.W. Burley, M. Thom, A. Sali, D.L. Kroetz, D.B. Goldstein, S.M. Sisodiya. Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia 48, 674-683, 2007. PubMedPDF
178.E. Feyfant, A. Sali, A. Fiser. Modeling mutations in protein structures. Protein Sci 16, 2030-2041, 2007. PubMedPDF
177.S.X. Wang, K.C. Pandey, J. Scharfstein, J. Whisstock, R.K. Huang, J. Jacobelli, R.J. Fletterick, P.J. Rosenthal, M. Abrahamson, L.S. Brinen, A. Rossi, A. Sali, J.H. McKerrow. The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family. Structure 15, 535-543, 2007. PubMedPDF
176.M.A. Carvalho, S.M. Marsillac, R. Karchin, S. Manoukian, S. Grist, R.F. Swaby, T.P. Urmenyi, E. Rondinelli, R. Silva, L. Gayol, L. Baumbach, R. Sutphen, J.L. Pickard-Brzosowicz, K.L. Nathanson, A. Sali, D. Goldgar, F.J. Couch, P. Radice, A.N. Monteiro. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res 67, 1494-1501, 2007. PubMedPDF
175.N. Eswar, A. Sali. Comparative Modeling of Drug Target Proteins. In: Volume 4 Computer-Assisted Drug Design, Comprehensive Medicinal Chemistry II. Ed: J. Taylor, D. Triggle, J.S. Mason, pp. 215-236, Elsevier Ltd, Oxford, UK, 2007.PDF
174.L. Kelly, R. Karchin, A. Sali. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac Symp Biocomput, 51-63, 2007. PubMedPDF
173.R. Karchin, A.N. Monteiro, S.V. Tavtigian, M.A. Carvalho, A. Sali. Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. PLoS Computational Biology 3, e26, 2007. PubMedPDF
172.N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Chapter 2, Unit 2.9, 2007. PubMedPDF
171.M.Y. Shen, A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Sci 15, 2507-2524, 2006. PubMedPDF
170.A. Colubri, A.K. Jha, M.Y. Shen, A. Sali, R.S. Berry, T.R. Sosnick, K.F. Freed. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol 363, 835-857, 2006. PubMedPDF
169.H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook. Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14, 1211-1217, 2006. PubMedPDF
168.T.D. Nguyen, J.M. Gow, L.W. Chinn, L. Kelly, H. Jeong, C.C. Huang, D. Stryke, M. Kawamoto, S.J. Johns, E. Carlson, T. Taylor, T.E. Ferrin, A. Sali, K.M. Giacomini, D.L. Kroetz. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacol Rev 58, 1-2, 2006. PubMedPDF
167.F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan. Protein complex compositions predicted by structural similarity. Nucleic Acids Res 34, 2943-2952, 2006. PubMedPDF
166.A. Rossi, M.A. Marti-Renom, A. Sali. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci 15, 2366-2380, 2006. PubMedPDF
165.N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Chapter 5, Unit 5.6, 2006. PubMedPDF
164.S. Dokudovskaya, R. Williams, D. Devos, A. Sali, B.T. Chait, M.P. Rout. Protease accessibility laddering: a proteomic tool for probing protein structure. Structure 14, 653-660, 2006. PubMedPDF
163.D. Eramian, M.Y. Shen, D. Devos, F. Melo, A. Sali, M.A. Marti-Renom. A composite score for predicting errors in protein structure models. Protein Sci 15, 1653-1666, 2006. PubMedPDF
162.D. Korkin, F.P. Davis, F. Alber, T. Luong, M.Y. Shen, V. Lucic, M.B. Kennedy, A. Sali. Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Computational Biology 2, e153, 2006. PubMedPDF
161.M. Topf, M.L. Baker, M.A. Marti-Renom, W. Chiu, A. Sali. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol 357, 1655-1668, 2006. PubMedPDF
160.U. Pieper, N. Eswar, F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, A. Sali. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34, D291-295, 2006. PubMedPDF
159.C. Lima, J. Puglisi, A. Sali, L. Szewczak. Editorial. Structure 14, 801, 2006.PDF
158.M.S. Madhusudhan, M.A. Marti-Renom, R. Sanchez, A. Sali. Variable gap penalty for protein sequence-structure alignment. Protein Engineering, Design & Selection 19, 129-133, 2006. PubMedPDF
157.D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali. Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A 103, 2172-2177, 2006. PubMedPDF
156.S.A. McMahon, J.L. Miller, J.A. Lawton, D.E. Kerkow, A. Hodes, M.A. Marti-Renom, S. Doulatov, E. Narayanan, A. Sali, J.F. Miller, P. Ghosh. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nature Structural Molecular Biology 12, 886-892, 2005. PubMedPDF
155.M. Topf, A. Sali. Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 15, 578-585, 2005. PubMedPDF
154.J.B. Bonanno, S.C. Almo, A. Bresnick, M.R. Chance, A. Fiser, S. Swaminathan, J. Jiang, F.W. Studier, L. Shapiro, C.D. Lima, T.M. Gaasterland, A. Sali, K. Bain, I. Feil, X. Gao, D. Lorimer, A. Ramos, J.M. Sauder, S.R. Wasserman, S. Emtage, K.L. D'Amico, S.K. Burley. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genom 6, 225-232, 2005. PubMedPDF
153.M.Y. Shen, F.P. Davis, A. Sali. The optimal size of a globular protein domain: A simple sphere-packing model. Chem Phys Lett 405, 224-228, 2005.PDF
152.D. Korkin, F.P. Davis, A. Sali. Localization of protein-binding sites within families of proteins. Protein Sci 14, 2350-2360, 2005. PubMedPDF
151.A. Sali, W. Chiu. Macromolecular assemblies highlighted. Structure 13, 339-341, 2005.PDF
150.J. Dvorak, M. Delcroix, A. Rossi, V. Vopalensky, M. Pospisek, M. Sedinova, L. Mikes, M. Sajid, A. Sali, J.H. Mckerrow, P. Horak, C.R. Caffrey. Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: Identification, characterization and putative role in migration and nutrition. International Journal of Parasitology 35, 895-910, 2005. PubMedPDF
149.S. Yasuda, N. Morokawa, G.W. Wong, A. Rossi, M.S. Madhusudhan, A. Sali, Y.S. Askew, R. Adachi, G.A. Silverman, S.A. Krilis, R.L. Stevens. Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22. Blood 105, 3893-3901, 2005. PubMedPDF
148.R. Karchin, M. Diekhans, L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21, 2814-2820, 2005. PubMedPDF
147.F.P. Davis, A. Sali. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21, 1901-1907, 2005. PubMedPDF
146.F. Alber, M.F. Kim, A. Sali. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13, 435-445, 2005. PubMedPDF
145.M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, M.i.n.-.y.i. Shen, A. Sali. Comparative Protein Structure Modeling. In: Proteomics Protocols Handbook. Ed: J.M. Walker, pp. 831-860, Humana Press Inc., Totowa, NJ, 2005.PDF
144.R. Karchin, L. Kelly, A. Sali. Improving functional annotation of non-synonomous SNPs with information theory. Pac Symp Biocomput, 397-408, 2005. PubMedPDF
143.M. Topf, M.L. Baker, B. John, W. Chiu, A. Sali. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol 149, 191-203, 2005. PubMedPDF
142.J. Espadaler, R. Aragues, N. Eswar, M.A. Marti-Renom, E. Querol, F.X. Aviles, A. Sali, B. Oliva. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A 102, 7151-7156, 2005. PubMedPDF
141.S.M. Maurer, A. Rai, A. Sali. Finding Cures for Tropical Diseases: Is Open Source an Answer? PLoS Medicine 1, e56, 2004. PubMedPDF
140.D. Devos, S. Dokudovskaya, F. Alber, R. Williams, B.T. Chait, A. Sali, M.P. Rout. Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biology 2, e380, 2004. PubMedPDF
139.R.B. Russell, F. Alber, P. Aloy, F.P. Davis, D. Korkin, M. Pichaud, M. Topf, A. Sali. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 14, 313-324, 2004. PubMedPDF
138.M. Jacobson, A. Sali. Comparative Protein Structure Modeling and Its Applications to Drug Discovery. In: Annual Reports in Medicinal Chemistry. Ed: J. Overington, 39, pp. 259-276, Inpharmatica Ltd., London, 2004.PDF
137.M.R. Chance, A. Fiser, A. Sali, U. Pieper, N. Eswar, G. Xu, J.E. Fajardo, T. Radhakannan, N. Marinkovic. High-throughput computational and experimental techniques in structural genomics. Genome Res 14, 2145-2154, 2004. PubMedPDF
136.S.M. Maurer, A. Rai, A. Sali. Finding Cures for Tropical Diseases: Is Open Source An Answer? In: Biotechnology: Essays From Its Heartland. Ed: L.y.n.n. Laboratory Yarris, June 2004, pp. 33-37, 2004.PDF
135.U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C.C. Huang, T.E. Ferrin, A. Sali. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32, D217-D222, 2004. PubMedPDF
134.S.M. Maurer, A. Rai, A. Sali. Finding Cures for Tropical Diseases: Is Open Source An Answer? Minnesota Journal of Law, Science & Technology 6, 169-175, 2004.PDF
133.B. John, A. Sali. Detection of homologous proteins by an intermediate sequence search. Protein Sci 13, 54-62, 2004. PubMedPDF
132.F. Alber, N. Eswar, A. Sali. Structure determination of macromolecular complexes by experiment and computation. Practical Bioinformatics, Ed: J.Bujnicki 15, 73-96, 2004.PDF
131.M.A. Marti-Renom, M.S. Madhusudhan, A. Sali. Alignment of protein sequences by their profiles. Protein Sci 13, 1071-1087, 2004. PubMedPDF
130.A. Rossi, Q. Deveraux, B. Turk, A. Sali. Comprehensive search for cysteine cathepsins in the human genome. Biol Chem 385, 363-372, 2004. PubMedPDF
129.N. Mirkovic, M.A. Marti-Renom, B.L. Weber, A. Sali, A.N. Monteiro. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res 64, 3790-3797, 2004. PubMedPDF
128.A. Fiser, A. Sali. ModLoop: automated modeling of loops in protein structures. Bioinformatics 19, 2500-2501, 2003. PubMedPDF
127.A. Sali. NIH workshop on structural proteomics of biological complexes. Structure 11, 1043-1047, 2003. PubMedPDF
126.M.A. Marti-Renom, A. Fiser, M.S. Madhusudhan, B. John, A.C. Stuart, N. Eswar, U. Pieper, M.-.Y. Shen, A. Sali. Modeling protein structure from its sequence. In: Current Protocols in Bioinformatics, V. 5, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., 2003.PDF
125.S.A. Lee, E.L. Shen, A. Fiser, A. Sali, S. Guo. The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons. Development 130, 2669-2679, 2003. PubMedPDF
124.H.X. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. Van Roey, R.K. Agrawal, S.C. Harvey, A. Sali, M.S. Chapman, J. Frank. Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement. Cell 113, 789-801, 2003. PubMedPDF
123.N. Eswar, B. John, N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, A. Sali. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res 31, 3375-3380, 2003. PubMedPDF
122.B. John, A. Sali. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 31, 3982-3992, 2003. PubMedPDF
121.I.Y.Y. Koh, V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, B. Rost. EVA: evaluation of protein structure prediction servers. Nucleic Acids Res 31, 3311-3315, 2003. PubMedPDF
120.A. Sali, R. Glaeser, T. Earnest, W. Baumeister. From words to literature in structural proteomics. Nature 422, 216-225, 2003. PubMedPDF
119.A. Fiser, A. Sali. Comparative Protein Structure Modeling. In: Protein Structure. Ed: D. Chasman, pp. 167-206, Marcel Dekker, Inc., 2003.PDF
118.M.A. Marti-Renom, B. Yerkovich, A. Sali. Modeling protein structure from its sequence. In: Current Protocols in Bioinformatics, V. 5 January Issue, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., Hoboken, NJ, 2003.PDF
117.V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, L. McMahan, A. Sali. ModView, visualization of multiple protein sequences and structures. Bioinformatics 19, 165-166, 2003. PubMedPDF
116.A. Fiser, A. Sali. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374, 461-491, 2003. PubMedPDF
115.G.M. Iverson, S. Reddel, E.J. Victoria, K.A. Cockerill, Y.X. Wang, M.A. Marti-Renom, A. Sali, D.M. Marquis, S.A. Krilis, M.D. Linnik. Use of single point mutations in domain I of beta(2)-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol 169, 7097-7103, 2002. PubMedPDF
114.M.A. Marti-Renom, B. Yerkovich, A. Sali. Comparative protein structure prediction. In: Current Protocols in Protein Science, pp. 2.9.1-2.9.22, John Wiley & Sons, 2002.PDF
113.Y. Yang, L.X. Li, G.W. Wong, S.A. Krilis, M.S. Madhusudhan, A. Sali, R.L. Stevens. RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs - Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function. J Biol Chem 277, 25756-25774, 2002. PubMedPDF
112.K.R. Rajashankar, M.R. Chance, S.K. Burley, J. Jiang, S.C. Almo, A.R. Bresnick, T. Dodatko, R. Huang, G. He, H. Chen, M. Sullivan, J. Toomey, R.A. Thirumuruhan, W.A. Franklin, A. Sali, U. Pieper, N. Eswar, V. Ilyin, L. McMahan. Structural Genomics at the National Synchrotron Light Source. NSLS Activity Report 2001 2, 28-32, 2002.PDF
111.M.R. Chance, A.R. Bresnick, S.K. Burley, J.S. Jiang, C.D. Lima, A. Sali, S.C. Almo, J.B. Bonanno, J.A. Buglino, S. Boulton, H. Chen, N. Eswar, G.S. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, L.K. Wang. Structural genomics: A pipeline for providing structures for the biologist. Protein Sci 11, 723-738, 2002. PubMedPDF
110.U. Pieper, N. Eswar, A.C. Stuart, V.A. Ilyin, A. Sali. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res 30, 255-259, 2002. PubMedPDF
109.A. Fiser, M. Feig, C.L. Brooks, A. Sali. Evolution and physics in comparative protein structure modeling. Accounts of Chemical Research 35, 413-421, 2002. PubMedPDF
108.A. Sali, M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost. Reply to Moult et al. Structure 10, 292-293, 2002.PDF
107.M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost, A. Sali. Reliability of assessment of protein structure prediction methods. Structure 10, 435-440, 2002. PubMedPDF
106.A.C. Stuart, V.A. Ilyin, A. Sali. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18, 200-201, 2002. PubMedPDF
105.F. Melo, R. Sanchez, A. Sali. Statistical potentials for fold assessment. Protein Sci 11, 430-448, 2002. PubMedPDF
104.J. Vernal, A. Fiser, A. Sali, M. Muller, J.J. Cazzulo, C. Nowicki. Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis. Biochem Biophys Res Commun 293, 633-639, 2002. PubMedPDF
103.D. Baker, A. Sali. Protein structure prediction and structural genomics. Science 294, 93-96, 2001. PubMedPDF
102.C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. Response to Paoli. Nat Struct Biol 8, 745, 2001.PDF
101.M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin. The third Georgia Tech - Emory international conference on bioinformatics: in silico biology; bioinformatics after human genome November 15-18, 2001, Atlanta, Georgia, USA. Bioinformatics 17, 859-861, 2001. PubMedPDF
100.G.W. Wong, S. Yasuda, M.S. Madhusudhan, L. Li, Y. Yang, S.A. Krilis, A. Sali, R.L. Stevens. Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells. J Biol Chem 276, 49169-49182, 2001. PubMedPDF
99.R. Beckmann, C.M.T. Spahn, N. Eswar, J. Helmers, P.A. Penczek, A. Sali, J. Frank, G. Blobel. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361-372, 2001. PubMedPDF
98.C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, J. Frank. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell 107, 373-386, 2001. PubMedPDF
97.J.B. Bonanno, C. Edo, N. Eswar, U. Pieper, M.J. Romanowski, V. Ilyin, S.E. Gerchman, H. Kycia, F.W. Studier, A. Sali, S.K. Burley. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A 98, 12896-12901, 2001. PubMedPDF
96.A. Sali. Target practice. Nat Struct Biol 8, 482-484, 2001. PubMedPDF
95.L.G. Barrientos, R. Campos-Olivas, J.M. Louis, A. Fiser, A. Sali, A.M. Gronenborn. 1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N. J Biomol NMR 19, 289-290, 2001. PubMedPDF
94.G.W. Wong, L. Li, M.S. Madhusudhan, S.A. Krilis, M.F. Gurish, M.E. Rothenberg, A. Sali, R.L. Stevens. Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases. J Biol Chem 276, 20648-20658, 2001. PubMedPDF
93.M.A. Marti-Renom, V.A. Ilyin, A. Sali. DBAli: a database of protein structure alignments. Bioinformatics 17, 746-747, 2001. PubMedPDF
92.V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, A. Fiser, F. Pazos, A. Valencia, A. Sali, B. Rost. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17, 1242-1243, 2001. PubMedPDF
91.S. Gopal, M. Schroeder, U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, J.E. Fajardo, N. Eswar, R. Sanchez, A. Sali, T. Gaasterland. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet 27, 337-340, 2001. PubMedPDF
90.C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. Crystal structures of ribosome anti-association factor IF6. Nat Struct Biol 7, 1156-1164, 2000. PubMedPDF
89.A. Fiser, R. Sanchez, F. Melo, A. Sali. Comparative protein structure modeling. In: Computational Biochemistry and Biophysics. Ed: M. Watanabe, B. Roux, A. Mackerell, O. Becker, pp. 275-312, Marcel Dekker, 2000.PDF
88.R. Sanchez, U. Pieper, F. Melo, N. Eswar, M.A. Marti-Renom, M.S. Madhusudhan, N. Mirkovic, A. Sali. Protein structure modeling for structural genomics. Nat Struct Biol 7, 986-990, 2000. PubMedPDF
87.S.K. Jin, S. Martinek, W.S. Joo, J.R. Wortman, N. Mirkovic, A. Sali, M.D. Yandell, N.P. Pavletich, M.W. Young, A.J. Levine. Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci U S A 97, 7301-7306, 2000. PubMedPDF
86.W. Liedtke, Y. Choe, M.A. Marti-Renom, A.M. Bell, C.S. Denis, A. Sali, A.J. Hudspeth, J.M. Friedman, S. Heller. Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor. Cell 103, 525-535, 2000. PubMedPDF
85.A. Fiser, R.K.G. Do, A. Sali. Modeling of loops in protein structures. Protein Sci 9, 1753-1773, 2000. PubMedPDF
84.G. Wu, A.G. McArthur, A. Fiser, A. Sali, M.L. Sogin, M. Muller. Core histones of the amitochondriate protist, Giardia lamblia. Mol Biol Evol 17, 1156-1163, 2000. PubMedPDF
83.R. Sanchez, A. Sali. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 143, 97-129, 2000. PubMedPDF
82.A.R. Dinner, A. Sali, L.J. Smith, C.M. Dobson, M. Karplus. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci 25, 331-339, 2000. PubMedPDF
81.R. Sanchez, U. Pieper, N. Mirkovic, P.I.W. de Bakker, E. Wittenstein, A. Sali. ModBase, a database of annotated comparative protein structure models. Nucleic Acids Res 28, 250-253, 2000. PubMedPDF
80.M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29, 291-325, 2000. PubMedPDF
79.C. Huang, G. Morales, A. Vagi, K. Chanasyk, M. Ferrazzi, C. Burklow, W.T. Qiu, E. Feyfant, A. Sali, R.L. Stevens. Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface. J Biol Chem 275, 351-358, 2000. PubMedPDF
78.P. Baldi, M. Borodovsky, S. Brunak, C. Burge, J. Fickett, S. Henikoff, E. Koonin, A. Sali, C. Sander, G. Stormo. The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function. Bioinformatics 15, 865-866, 1999. PubMedPDF
77.A. Sali. Functional links between proteins. Nature 402, 23, 25-26, 1999. PubMedPDF
76.A. Sali, J. Kuriyan. Challenges at the frontiers of structural biology (Reprinted from Trends in Biochemical Science, vol 12, Dec., 1999). Trends Cell Biol 9, M20-M24, 1999. PubMedPDF
75.S.K. Burley, S.C. Almo, J.B. Bonanno, M. Capel, M.R. Chance, T. Gaasterland, D. Lin, A. Sali, F.W. Studier, S. Swaminathan. Structural genomics: beyond the human genome project. Nat Genet 23, 151-157, 1999. PubMedPDF
74.G.W. Wong, Y. Tang, E. Feyfant, A. Sali, L. Li, Y. Li, C. Huang, D.S. Friend, S.A. Krilis, R.L. Stevens. Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension. J Biol Chem 274, 30784-30793, 1999. PubMedPDF
73.J.M. Miwa, I. Ibanez-Tallon, G.W. Crabtree, R. Sanchez, A. Sali, L.W. Role, N. Heintz. lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS. Neuron 23, 105-114, 1999. PubMedPDF
72.T. Nagata, V. Gupta, D. Sorce, W.Y. Kim, A. Sali, B.T. Chait, K. Shigesada, Y. Ito, M.H. Werner. Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain. Nat Struct Biol 6, 615-619, 1999. PubMedPDF
71.G. Wu, A. Fiser, B. ter Kuile, A. Sali, M. Muller. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proc Natl Acad Sci U S A 96, 6285-6290, 1999. PubMedPDF
70.R. Sanchez, A. Sali. Comparative protein structure modeling in genomics. Journal of Computational Physics 151, 388-401, 1999.PDF
69.R. Sanchez, A. Sali. MODBASE: A database of comparative protein structure models. Bioinformatics 15, 1060-1061, 1999. PubMedPDF
68.A. Sali. 100,000 protein structures for the biologist. Nat Struct Biol 5, 1029-1032, 1998. PubMedPDF
67.R. Sanchez, A. Sali. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A 95, 13597-13602, 1998. PubMedPDF
66.E. Wolf, A. Vassilev, Y. Makino, A. Sali, Y. Nakatani, S.K. Burley. Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell 94, 439-449, 1998. PubMedPDF
65.A. Gutin, A. Sali, V. Abkevich, M. Karplus, E. Shakhnovich. Temperature dependence of the folding rate in a simple protein model: Search for a glass transition. J Chem Phys 108, 6466-6483, 1998.PDF
64.D.A. Kandiah, A. Sali, Y. Sheng, E.J. Victoria, D.M. Marquis, S.M. Coutts, S.A. Krilis. Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects. Advanced Immunology Journal 70, 507-563, 1998. PubMedPDF
63.C. Huang, A. Sali, R.L. Stevens. Regulation and function of mast cell proteases in inflammation. J Clin Immunol 18, 169-183, 1998. PubMedPDF
62.C.M. Dobson, A. Sali, M. Karplus. Protein folding: A perspective from theory and experiment. Angewandte Chemie Int Ed 37, 868-893, 1998.PDF
61.Y. Sheng, S.A. Krilis, A. Sali. Site-directed mutagenesis of recombinant human beta 2-glycoprotein I. Effect of phospholipid binding and anticardiolipin antibody activity. Ann N Y Acad Sci 815, 331-333, 1997. PubMedPDF
60.R. Sanchez, A.Ya. Badretdinov, E. Feyfant, A. Sali. Homology protein structure modeling. Transactions of the American Crystallographic Association 32, 81-91, 1997.PDF
59.B. Guenther, R. Onrust, A. Sali, M. O'Donnell, J. Kuriyan. Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91, 335-345, 1997. PubMedPDF
58.R. Sanchez, A. Sali. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins Suppl 1, 50-58, 1997. PubMedPDF
57.J.E. Hunt, D.S. Friend, M.F. Gurish, E. Feyfant, A. Sali, C. Huang, N. Ghildyal, S. Stechschulte, K.F. Austen, R.L. Stevens. Mouse mast cell protease 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells. J Biol Chem 272, 29158-29166, 1997. PubMedPDF
56.D. Koulich, M. Orlova, A. Malhotra, A. Sali, S.A. Darst, S. Borukhov. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J Biol Chem 272, 7201-7210, 1997. PubMedPDF
55.R. Sanchez, A. Sali. Advances in comparative protein-structure modelling. Curr Opin Struct Biol 7, 206-214, 1997. PubMedPDF
54.R. Sanchez, A. Sali. Comparative protein modeling as an optimization problem. Journal of Molecular Structure (Theochem) 398, 489-496, 1997.PDF
53.C. Huang, G.W. Wong, N. Ghildyal, M.F. Gurish, A. Sali, R. Matsumoto, W.T. Qiu, R.L. Stevens. The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma. J Biol Chem 272, 31885-31893, 1997. PubMedPDF
52.M. Russel, N.A. Linderoth, A. Sali. Filamentous phage assembly: variation on a protein export theme. Gene 192, 23-32, 1997. PubMedPDF
51.S. Wu, H. de Lencastre, A. Sali, A. Tomasz. A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing. Microbial Drug Resistance 2, 277-286, 1996. PubMedPDF
50.A.R. Dinner, A. Sali, M. Karplus. The folding mechanism of larger model proteins: role of native structure. Proc Natl Acad Sci U S A 93, 8356-8361, 1996. PubMedPDF
49.L.Z. Xu, R. Sanchez, A. Sali, N. Heintz. Ligand specificity of brain lipid-binding protein. J Biol Chem 271, 24711-24719, 1996. PubMedPDF
48.N. Ghildyal, D.S. Friend, R.L. Stevens, K.F. Austen, C. Huang, J.F. Penrose, A. Sali, M.F. Gurish. Fate of two mast cell tryptases in V3 mastocytosis and normal BALB/c mice undergoing passive systemic anaphylaxis: prolonged retention of exocytosed mMCP-6 in connective tissues, and rapid accumulation of enzymatically active mMCP-7 in the blood. The Journal of Experimental Medicine 184, 1061-1073, 1996. PubMedPDF
47.Y. Sheng, A. Sali, H. Herzog, J. Lahnstein, S.A. Krilis. Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity. J Immunol 157, 3744-3751, 1996. PubMedPDF
46.M. Karplus, A. Sali, E. Shakhnovich. Kinetics of protein folding. Nature 373, 664-665, 1995.PDF
45.A. Sali. Modeling mutations and homologous proteins. Curr Opin Biotechnol 6, 437-451, 1995. PubMedPDF
44.A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, M. Karplus. Evaluation of comparative protein modeling by MODELLER. Proteins 23, 318-326, 1995. PubMedPDF
43.A. Sali, E. Shakhnovich, M. Karplus. Thermodynamics and kinetics of protein folding from lattice Monte Carlo simulations. In: DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Ed: D. Shalloway, G. Xue, P. Pardalos, 23, pp. 199-213, American Mathematical Society, 1995.PDF
42.A. Sali, E. Shakhnovich, M. Karplus. Protein Folding Studied by Monte Carlo Simulations. In: Protein Folds: A Distance Based Approach. Ed: H. Bohr, S. Brunak, pp. 202-216, CRC Press Inc., 1995.PDF
41.A. Sali. Comparative protein modeling by satisfaction of spatial restraints. Mol Med Today 1, 270-277, 1995. PubMedPDF
40.R. Matsumoto, A. Sali, N. Ghildyal, M. Karplus, R.L. Stevens. Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans. J Biol Chem 270, 19524-19531, 1995. PubMedPDF
39.X.D. Wu, B. Knudsen, S.M. Feller, J. Zheng, A. Sali, D. Cowburn, H. Hanafusa, J. Kuriyan. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the amino-terminal SH3 domain of c-Crk. Structure 3, 215-226, 1995. PubMedPDF
38.A. Sali. MODELLER: Implementing 3D protein modeling. In: mc^2, 2, pp. 5, Molecular Simulations Inc., 1995.PDF
37.M. Karplus, A. Caflisch, A. Sali, E. Shakhnovich. Protein dynamics: From the native to the unfolded state and back again. In: Modelling of Biomolecular Structures and Mechanisms. Ed: A.Pullmanet al, pp. 69-84, Kluwer Academic Publishers, 1995.PDF
36.M. Karplus, A. Sali. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 5, 58-73, 1995. PubMedPDF
35.A. Dinner, A. Sali, M. Karplus, E. Shakhnovich. Phase diagram of a model protein derived by exhaustive enumeration of the conformations. J Chem Phys 101, 1444-1451, 1994.PDF
34.A. Sali, E. Shakhnovich, M. Karplus. How does a protein fold? Nature 369, 248-251, 1994. PubMedPDF
33.A. Sali, E. Shakhnovich, M. Karplus. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J Mol Biol 235, 1614-1636, 1994. PubMedPDF
32.A. Sali, J.P. Overington. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci 3, 1582-1596, 1994. PubMedPDF
31.A. Sali, T. Blundell. Comparative protein modeling by statisfaction of spatial restraints. In: Protein Structure by Distance Analysis. Ed: H. Bohr, S. Brunak, pp. 64-86, TECH UNIV DENMARK, CTR BIOL SEQUENCE ANAL, LYNGBY, DENMARK, 1994.PDF
30.A. Sali, R. Matsumoto, H.P. McNeil, M. Karplus, R.L. Stevens. Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes. J Biol Chem 268, 9023-9034, 1993. PubMedPDF
29.A. Sali, T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234, 779-815, 1993. PubMedPDF
28.J.P. Overington, Z.Y. Zhu, A. Sali, M.S. Johnson, R. Sowdhamini, G.V. Louie, T.L. Blundell. Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins. Biochem Soc Trans 21 ( Pt 3), 597-604, 1993. PubMedPDF
27.M.S. Johnson, J.P. Overington, A. Sali, T.L. Blundell. From the comparative analysis of proteins to similarity-based modelling. In: Computer Modelling of Biomolecular Processes. Ed: V.A. Ratner, N.A. Kolchanov, pp. 191-196, Nova Science Publishers, 1992.PDF
26.J. Overington, D. Donnelly, M.S. Johnson, A. Sali, T.L. Blundell. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci 1, 216-226, 1992. PubMedPDF
25.Z.Y. Zhu, A. Sali, T.L. Blundell. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng 5, 43-51, 1992. PubMedPDF
24.B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell, R.L. Rosati, B.W. Dominy, D.B. Damon, D.J. Hoover. Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases. Protein Sci 1, 322-328, 1992. PMC2142209 PubMedPDF
23.A. Sali, B. Veerapandian, J.B. Cooper, D.S. Moss, T. Hofmann, T.L. Blundell. Domain flexibility in aspartic proteinases. Proteins 12, 158-170, 1992. PubMedPDF
22.A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. From modelling homologous proteins to prediction of structure. In: Protein design and the development of new therapeutics and vaccines. Ed: J.M. Goodfellow, D.S. Moss, pp. 231-245, Ellis Horwood Ltd., 1991.PDF
21.T.L. Blundell, J.B. Cooper, D. Donnelly, H. Driessen, Y. Edwards, F. Eisenmenger, C. Frazao, M. Johnson, K. Niefind, M. Newman, J. Overington, A. Sali, C. Slingsby, V. Nalini, Z.Y. Zhu. Patterns of sequence variation in families of homologous proteins. In: Methods in Protein Sequence Analysis. Ed: H. Jornval, J.O. Hoog, A.M. Gustavsson, pp. 373-385, Birkhauser Verlag, Basel, Switzerland, 1991.PDF
20.T.L. Blundell, J.B. Cooper, A. Sali, Z.Y. Zhu. Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases. Adv Exp Med Biol 306, 443-453, 1991. PubMed
19.T.L. Blundell, M.S. Johnson, J.P. Overington, A. Sali. Knowledge-based protein modeling and the design of novel molecules. In: Protein design and the development of new therapeutics and vaccines. Ed: J.B. Hook, G. Poste, pp. 209-227, Plenum Press, New York, NY, 1990.PDF
18.M.S. Johnson, J. Overington, A. Sali, Z. Zhu, D. Donnelly, P. Thomas, A. McLeod, R. Goold, C. Topham, T.L. Blundell. From comparative structure analysis to protein engineering: Knowledge-based protein modelling and design. Fresenius Journal of Analytic Chemistry 337, 1-3, 1990.PDF
17.M.S. Johnson, J.P. Overington, A. Sali. Knowledge-based protein modelling: Human plasma kallikrein and human neutrophil defensin. In: Chemistry: Techniques Structure and Function. Ed: J.J. Vilafranca, pp. 567-574, Academic Press, Inc., 1990.PDF
16.M.S. Johnson, A. Sali, T.L. Blundell. Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol 183, 670-690, 1990. PubMedPDF
15.J.P. Overington, M.S. Johnson, C. Topham, A. McLeod, A. Sali, Z.Y. Zhu, L. Sibanda, T.L. Blundell. Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure. Curr Sci 59, 867-874, 1990.PDF
14.J. Overington, M.S. Johnson, A. Sali, T.L. Blundell. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Procedures in Biological Science 241, 132-145, 1990. PubMedPDF
13.B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell. X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution. J Mol Biol 216, 1017-1029, 1990. PubMedPDF
12.A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. From Comparisons of protein sequences and structures to protein modelling and design. Trends Biochem Sci 15, 235-240, 1990. PubMedPDF
11.A. Sali, T.L. Blundell. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 212, 403-428, 1990. PubMedPDF
10.T.L. Blundell, D. Carney, T. Hubbard, M.S. Johnson, A. McLeod, J.P. Overington, A. Sali, M.S. Sutcliffe, P. Thomas. Knowledge-based protein modelling and design. In: Advances in Protein Design: International Workshop 1988 GBF Monographs. Ed: H. Bloecker, J. Collins, R.D. Schmid, D. Schomburg, 12, pp. 39-43, VCH, 1989.PDF
9.T.L. Blundell, G. Elliott, S.P. Gardner, T. Hubbard, S. Islam, M. Johnson, D. Mantafounis, P. Murrayrust, J. Overington, J.E. Pitts, A. Sali, B.L. Sibanda, J. Singh, M.J.E. Sternberg, M.J. Sutcliffe, J.M. Thornton, P. Travers. Protein engineering and design. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 324, 447-460, 1989. PubMedPDF
8.A. Sali, B. Veerapandian, J.B. Cooper, S.I. Foundling, D.J. Hoover, T.L. Blundell. High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme. Embo Journal 8, 2179-2188, 1989. PubMedPDF
7.V. Turk, R. Jerala, B. Lenarcic, A. Sali. Structural and functional aspects of human cathepsins B. In: Intracellular Proteolysis: Mechanisms and Regulations. Ed: N. Katunuma, E. Kominami, pp. 27 -37, Japan Scientific Societies Press, 1989.PDF
6.T. Lah, I. Kregar, A. Sali, B. Lenarcic, M. Kotnik, V. Kostka, V. Turk. Circular dichroism studies of different aspartyl proteinases and their interactions with pepstatin. Periodicum Biologorum 90, 31-38, 1988.PDF
5.A. Sali, V. Turk. Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases. Biol Chem Hoppe Seyler 368, 493-499, 1987. PubMedPDF
4.M. Kotnik, A. Sali, J. Kos, B. Turk, V. Turk. Nova metoda za hitro dolocanje kineticnih konstant pri interakciji encima s kompetitivnim inhibitorjem (A new method for rapid determination of kinetic constants for competitive inhibition of enzymes). Vestnik Slovenskaga Kemijskega Drustva 34, 369-377, 1987.PDF
3.V. Turk, J. Brzin, B. Lenarcic, A. Sali, W. Machleidt. Human stefins and cystatis: their properties and structural relationships. In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 429-442, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.PDF
2.B. Lenarcic, A. Ritonja, A. Sali, M. Kotnik, V. Turk, W. Machleidt. Properties and structure of human spleen stefin B - a low molecular weight protein inhibitor of cysteine proteinases. In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 473-488, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.PDF
1.M. Renko, A. Sali, V. Turk, M. Pokomy, I. Kregar. A neutral metalloproteinase from Streptomyces rimosus. Vestnik Slovenskega Kemijskega Drustva 32/2, 161-173, 1985.PDF
Andrej Sali, PhD, Professor, Department of Bioengineering and Therapeutic Sciences; Department of Pharmaceutical Chemistry; School of Pharmacy, University of California at San Francisco, UCSF MC 2552, Mission Bay, Byers Hall, 1700 4th Street, Suite 503B, San Francisco, CA 94143, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, Web https://salilab.org

This is not an official UCSF website. The opinions or statements expressed herein should not be taken as a position of or endorsement by the University of California, San Francisco.