Publications
461. Mondal D, Kumar V, Satler T, Ramachandran R, Saltzberg D, Chemmama I, Pilla KB, Echeverria I, Webb BM, Gupta M, Verba KA, Sali A. Recognizing amino acid sidechains in a medium resolution cryo-electron density map. bioRxiv, 2024.
460. Peulen TO, Hemmen K, Greife A, Webb BM, Felekyan S, Sali A, Seidel CAM, Sanabria H, Heinze KG. tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling. Bioinformatics, in press, 2024.
459. Latham AP, Tempkin JOB, Otsuka S, Zhang W, Ellenberg J, Sali A. Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex. bioRxiv, 2024. PMCID11326192
458. Hanke CA, Westbrook JD, Webb BM, Peulen T, Lawson CL, Sali A, Berman HM, Seidel CAM, Vallat B. Making fluorescence-based integrative structures and associated kinetic information accessible. Nat Meth, online ahead of print, 2024.
457. Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon J, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. in press, 2024. PMCID11142054
456. Giacomini K, Yee SW, Peral LF, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske M, Handin N, Artegoitia V, Lara G, Chien H, Zhou X, Dainat J, Zalevsky A, Sali A, Brand C, Capra J, Artursson P, Newman J, Marques-Bonet T, Wolfreys F, Yang J, Gestwicki J. Illuminating the Function of the Orphan Transporter, SLC22A10, in Humans and Other Primates. Nat Comm, in press, 2024. PMCID10543398
455. Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The Molecular Architecture of the Nuclear Basket. Cell 187, 5267-5281, 2024. PMCID11416316
454. Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J. Mol. Biol. 436, 168546, 2024. PMCID11377171
453. Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. Integrative spatiotemporal map of nucleocytoplasmic transport. in press, 2024. PMCID10802240
452. Li W, Li A, Yu B, Zhang X, Liu X, White KL, Stevens RC, Baumeister W, Sali A, Jasnin M, Sun L. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Nat Commun 15, 1311, 2024. PMCID10861521
451. Pourmal S, Green E, Bajaj R, Chemmama I, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Stroud RM, Kroetz DL. Structural Basis of Prostaglandin Efflux by MRP4. Nat Struct Mol Biol 31, 621-632, 2024. PMCID11145372
450. Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. eLife 12, RP89423, 2024. PMCID11076045
448. Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature 626, 194-206, 2023. PMCID10830420
447. Lin Z, Schaefer K, Lui I, Yao Z, Fossati AA, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. in press, 2023.
446. Peulen TO, Sali A. Bayesian Fluorescence Framework for integrative modeling of biomolecules. in press, 2023.
445. Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. Implications of a multiscale structure of the yeast nuclear pore complex. Mol. Cell 83, 3283-3302.e5, 2023. PMCID10630966
444. Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol 30, 296-308, 2023. PMCID10312659
443. Burns KH, Smail B, Jiang H, Zalevsky A, Dai N, Trachman RJ, Guan S, Sali A, Taylor MS, LaCava J. Robust cleavage of mismatched DNA by the LINE-1 endonuclease. J Biol Chem, in press, 2023.
442. Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. in press, 2023. PMCID10103940
441. Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. J. Mol. Biol. 435, 168021, 2023. PMCID10293049
440. Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature 613, 575-581, 2023. PMCID9849139
439. Echeverria I, Braberg H, Krogan NJ, Sali A. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J 290, 2565-2575, 2023. PMCID9481981
438. Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. 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
437. Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young J, Zardecki C. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 12, 1425, 2022. PMCID9599165
436. Opoku-Nsiah KA, de la Pena AH, Williams SK, Chopra N, Sali A, Lander GC, Gestwicki JE. The YΦ Motif Defines the Structure-Activity Relationships of Human 20S Proteasome Activators. Nat Commun 13, 1226, 2022. PMCID8907193
435. Burley S, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig P, Crichlow G, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt J, Ganesan S, Ghosh S, Goodsell D, Green RK, Guranovic V, Henry J, Hudson B, Lawson C, Liang Y, Lowe R, Peisach E, Persikova I, Piehl D, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook J, Whetstone S, Young J, Zalevsky A, Zardecki C. RCSB Protein Data Bank: Tools for visualizing and understanding biological macromolecules in 3D. Prot Sci 31, e4482, 2022. PMCID9667899
434. Li A, Zhang X, Singla J, White K, Loconte V, Hu C, Zhang C, Li S, Li W, Francis JP, Wang C, Sali A, Sun L, He X, Stevens RC. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. PLoS One 17, e0265567, 2022. PMCID8947144
433. Rafiei A, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard GJ, Schriemer DC. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 11, e66975, 2022. PMCID9122500
432. Guo A, Zhang J, He B, Li A, Sun T, Li C, Wang J, Tai R, Fan J, Sali A, Stevens RC, Jiang H. Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic β cells. Proc Natl Acad Sci USA 119, e2202695119, 2022. PMCID9371705
431. Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. Integration of software tools for integrative modeling of biomolecular systems. J. Struct. Biol. 214, 107841, 2022. PMCID9278553
430. Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Le Gros M, White KL, Larabell CA. Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure 30, 510-521, 2022. PMCID9013509
429. Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali S, Condello C, DeGrado WF. Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ. Proc Natl Acad Sci USA 119, e2114486119, 2022. PMCID8812518
428. Braberg H, Echeverria I, Kaake R, Sali A, Krogan N. From systems to structure — using genetic data to model protein structures. Nat Rev Genet 23, 342-354, 2022. PMCID8744059
427. Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex. Cell 185, 361-378, 2022. PMCID8928745
426. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C, Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Goodsell DS, Ghosh S, Green RK, Guranovic V, Henry J, Hudson BP, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Whetstone S, Young JY, Zardecki C. 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
425. Li A, Zhang S, Loconte V, Liu Y, Ekman A, Thompson GJ, Sali A, Stevens RC, White K, Singla J, Sun L. An Intensity-based Post-processing Tool for 3D Instance Segmentation of Organelles in Soft X-ray Tomograms. PLoS One 17, e0269887, 2022. PMCID9436087
424. Huang F, Nguyen TTT, Echeverria I, Ramachandran R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. eLife 10, e68473, 2021. PMCID8648303
423. Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. IMProv: A Resource for Crosslink-Driven Structure Modeling that Accommodates Protein Dynamics. Mol Cell Prot 20, 100139, 2021. PMCID8452774
422. Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Andrej Sali A, Krogan NJ. 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
421. Sali A. From integrative structural biology to cell biology. J. Biol. Chem., 100743, 2021. PMCID8203844
420. Vallat B, Webb B, Fayazi M, Voinea S, Tangmunarunkit H, Ganesan SJ, Lawson CL, Westbrook JD, Kesselman C, Sali A, Berman HM. New system for archiving integrative structures. Acta Cryst D 77, 1486-1496, 2021. PMCID8647179
419. Webb B, Sali A. Protein Structure Modeling with MODELLER. Meth Mol Biol 2199, 239-255, 2021.
418. Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure 29, 1-12, 2021. PMCID8675206
417. Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. eLife 10, e73027, 2021. PMCID8043454
416. Brilot A, Lyon A, Zelter A, Viswanath S, Maxwell A, Yabut KCB, MacCoss M, Eric Muller E, Sali A, Davis TN, Agard DA. CM1-driven assembly and activation of Yeast γ-Tubulin Small Complex underlies microtubule nucleation. eLife 10, e65168, 2021. PMCID8099430
415. Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Pilla KB, Singla J, Wang C, Zha J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A. Bayesian metamodeling of complex biological systems across varying representations. Proc Natl Acad Sci USA 118, e2104559118, 2021. PMCID8536362
414. Yu Y, Li S, Ser Z, Sanyal T, Choi K, Wan B, Kuang H, Sali A, Kentsis A, Patel DJ, Zhao X. Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Proc. Natl. Acad. Sci. 118, e2026844118, 2021. PMCID8126833
413. Salcedo EC, Winter MB, Khuri N, Knudsen GM, Sali A, Craik CS. Global Protease Activity Profiling Identifies HER2-Driven Proteolysis in Breast Cancer. ACS Chem. Biol. 16, 712-723, 2021.
412. Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A. Using Integrative Modeling Platform to Compute, Validate, and Archive a Model of a Protein Complex Structure. Prot Sci 30, 250-261, 2021. PMCID7737781
411. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow G, Christie CH, Dalenberg K, Di Costanzo L, Duarte JM, Dutta S, Feng Z, Ganesan S, Goodsell DS, Ghosh S, Green RK, Guranović V, Guzenko D, Hudson BP, Lawson CL, Liang Y, Lowe R, Namkoong H, Peisach E, Persikova I, Randle C, Rose A, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Tao Y, Voigt M, Westbrook JD, Young JY, Zardecki C, Zhuravleva M. 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
410. Tran TH, Nguyen JV, Stecula A, Akutagawa J, Moorman AV, Braun BS, Sali A, Mullighan CG, Shah NP, Dai Y, Devidas M, Roberts KG, Smith CC, Loh ML. 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
409. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ, Consortium QCRG Structural, Consortium Zoonomia. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 370, 2020. PMCID7808408
408. White KL, Singla J, Loconte V, Chen JH, Ekman A, Sun L, Zhang X, Francis JP, Li A, Lin W, Tseng K, McDermott G, Alber F, Sali A, Larabell C, Stevens RC. Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Sci Adv 6, 2020. PMCID7725475
407. Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong M, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure 28, 1259-1268, 2020.
406. Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor , D , Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. Genetic interaction mapping informs integrative structure determination of protein complexes. Science 370, 2020. PMCID7946025
405. Qiao Y, Wang Z, Tan F, Chen J, Lin J, Yang J, Li H, Wang X, Sali A, Zhang L, Zhong G. Enhancer Reprogramming within Pre-existing Topologically Associated Domains Promotes TGF-β-Induced EMT and Cancer Metastasis. Mol Ther 28, 2083-2095, 2020. PMCID7474343
404. Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J. Cell Biol. 219, 2020. PMCID7659715
403. Kwon Y, Kaake R, Echeverria I, Suarez M, Shamsabadi MK, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. Structural Basis of CD4 Downregulation by HIV-1 Nef. Nat Struct Mol Biol, 2020. PMCID7483821
402. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O’Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459-468, 2020. PMCID7431030
401. Ganesan SJ, Feyder MJ, Chemmama IE, Fang F, Rout MP, Chait BT, Shi Y, Munson M, Sali A. Integrative Structure and Function of the Yeast Exocyst Complex. Protein Sci. 29, 1486-1501, 2020. PMCID7255525
400. Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L. 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
399. Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A. 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
398. Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Wah Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips Jr GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models And Data: Outcomes From A Workshop On Archiving Integrative Structures. Structure 27, 1745-1759, 2019. PMCID7108332
397. Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. 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
396. Vallat B, Webb B, Westbrook J, Sali A, Berman HM. Archiving and Disseminating Integrative Structure Models. J. Biomol. NMR 73, 385-398, 2019. PMCID6692293
395. Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell 177, 1384-1403, 2019. PMCID6810593
394. Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. Modeling biological complexes using Integrative Modeling Platform. Methods Mol. Biol. 2022, 353-377, 2019.
393. Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 8, e43630, 2019. PMCID6453568
392. Viswanath S, Sali A. Optimizing model representation for integrative structure determination of macromolecular assemblies. Proc Natl Acad Sci USA, pii: 201814649, 2018. PMCID6329962
391. Jishage M, Yu X, Shi Y, Ganesan SJ, Chen WY, Sali A, Chait BT, Asturias FJ, Roeder RG. Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol 25, 859-867, 2018. PMCID6298426
390. Gaber A, Kim SJ, Kaake RM, Bencina M, Krogan N, Sali A, Pavsic M, Lenarcic B. EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Sci Rep 8, 13269, 2018. PMCID6125409
389. Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R. Bayesian weighing of electron cryo-microscopy data for integrative structural modeling. Structure, pii: S0969-2126(18)30337-X, 2018. PMCID6779587
388. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug & Play” Domain. Methods Enzymol. 606, 1-71, 2018. PMCID6445391
387. Lyon A, Zelter A, Viswanath S, Maxwell A, Johnson R, Yabut KCB, MacCoss M, Davis TN, Muller E, Sali A, Agard DA. Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly. submitted.
386. Singla J, McClary KM, White KL, Alber F, Sali A, Stevens RC. Opportunities and challenges in building a spatiotemporal multi-scale model of the human pancreatic β-cell. Cell 173, 11-19, 2018. PMCID6014618
385. Vallat B, Webb B, Westbrook J, Sali A, Berman HM. Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules. Structure 26, 894-904.e2, 2018. PMCID5990459
384. Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan J, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. Integrative Structure and Functional Anatomy of a Nuclear Pore Complex. Nature 555, 475-482, 2018. PMCID6022767
383. Guy AJ, Irani V, Beeson JG, Webb B, Sali A, Richards JS, Ramsland PA. Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. Sci Rep 8, 4355, 2018. PMCID5847524
382. Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O’Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. Prediction of enzymatic pathways by integrative pathway mapping. eLife 7, e31097, 2018. PMCID5788505
381. Yoshizawa T, Ali R, Fung HYJ, Burke KA, Lin Y, Kim SJ, Jiou J, Soniat M, Oldenbourg R, Sali A, Fawzi NL, Rosen MK, Chook YM. Nuclear import receptor inhibits phase separation of FUS through binding to multiple sites. Cell 173, 693-705, 2018. PMCID6234985
380. Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the Integrative Modeling Platform. Prot Sci 27, 245-258, 2018. PMCID5734277
379. Schneidman-Duhovny D, Khuri N, Dong GQ, Winter MB, Shifrut E, Friedman N, Craik CS, Pratt KP, Paz P, Aswad F, Sali A. Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PLoS ONE 13, e0206654, 2018. PMCID6219782
378. Winter MB, La Greca F, Arastu-Kapur S, Cimermancic P, Buchholz TJ, Caiazza F, Anderl JL, Ravalin M, Bohn MF, Sali A, O’Donoghue AJ, Craik CS. Immunoproteasome Functions Explained by Divergence in Cleavage Specificity and Regulation. eLife 6, e27364, 2017. PMCID5705213
377. Viswanath S, Chemmama I, Cimermancic P, Sali A. Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures. Biophys. J. 113, 2344-2353, 2017. PMCID5768525
376. Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol. Biol. Cell 28, 3298-3314, 2017. PMCID5687031
375. Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kriby NM, Kwan AH, Perez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 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
374. Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models. Structure 25, 1317-1318, 2017. PMCID5821105
373. Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. 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
372. Stecula A, Schlessinger A, Giacomini K, Sali A. Human concentrative nucleoside transporter 3 (hCNT3, SLC28A3) forms a cyclic homotrimer. Biochemistry 56, 3475-3483, 2017. PMCID6917504
371. Manna PT, Obado S, Boehm C, Gadelha C, van Miero G, Sali A, Chait B, Rout M, Field MC. Lineage-specific proteins essential for endocytosis in trypanosomes. J. Cell Sci. 130, 1379-1392, 2017. PMCID5399782
370. Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure 25, 434-445, 2017. PMCID5342941
369. Webb B, Sali A. Protein structure modeling with MODELLER. In: Meth Mol Biol, 1654, pp. 39-54, 2017.
368. Chen EC, Khuri N, Liang X, Stecula A, Chien H, Yee SW, Huang Y, Sali A, Giacomini KM. Discovery of competitive and non-competitive ligands of the organic cation transporter 1 (OCT1; SLC22A1). J. Med. Chem. 60, 2685-2696, 2017.
367. Chen A, Vieth M, Timm D, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Lu J, Liu L. Reconstruction of 3D structures of MET Antibodies from Electron Microscopy 2D Class Averages. PloS One 12, e0175758, 2017. PMCID5391116
366. Khuri N, Zur A, Wittwer M, Lin L, Yee SW, Sali A, Giacomini K. Computational Discovery And Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1. J Chem Inf Model 57, 1402-1413, 2017.
365. Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics 16, 840-854, 2017. PMCID5417825
364. Jahangiri A, Han SW, Sidorov MK, Chen W, Rick J, Schneidman-Duhovny D, Mascharak S, De Lay M, Wagner JR, Imber B, Flanigan PM, Chandra A, Kuang R, Castro BA, Lu K, Bergers G, Sali A, Weiss WA, Aghi MK. Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer. Proc Natl Acad Sci USA 114, E8685-E8694, 2017. PMCID5642678
363. Wang X, Chemmama IE, Yu C, Huszagh A, Xu Y, Viner R, Block SA, Cimermancic P, Rychnovsky S, Ye Y, Sali A, Huang L. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J. Biol. Chem. 292, 16310-16320, 2017. PMCID5625060
362. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. In: Curr Protoc Bioinformatics, 54, pp. 5.6.1-5.6.37, John Wiley and Sons, 2016. PMC5031415
361. Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. 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
360. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 167, 1215-1228, 2016. PMCID5130164
359. Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. 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
358. Barkan DT, Cheng X, Celino H, Tran T, Bhandari A, Craik CS, Sali A, Smythe ML. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics 17, 481, 2016. PMCID5120537
357. Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. Simple rules for passive diffusion through the nuclear pore complex. J. Cell Biol. 215, 57-76, 2016. PMCID5057280
356. Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife 5, e15910, 2016. PMCID5072841
355. Watts JC, Giles K, Saltzberg DJ, Dugger BN, Patel S, Oehler A, Bhardwaj S, Sali A, Prusiner SB. Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions. J. Virol. 90, 9558-9569, 2016. PMCID5068510
354. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. In: Curr Protoc Protein Sci, 86, pp. 2.9.1-2.9.37, John Wiley and Sons, 2016.
353. Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J. Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modelling. Mol Cell Proteomics 15, 2730-2743, 2016. PMCID4974347
352. Schneidman D, Hammel M, Tainer J, Sali A. 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
351. Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci USA 113, E2489-97, 2016. PMCID4983827
350. Lensink MF, Velankar S, Kryshtafovych A, Huang S, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Lee GR, Seok C, Qin S, Zhou H, Ritchie DW, Maigret B, Devignes M, Ghoorah A, Torchala M, Chaleil RAG, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JPGLM, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond ASJ, Visscher K, Kastritis PL, Bonvin AMJJ, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim H, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Burman SSR, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. 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
349. Sprowl J, Ong SS, Gibson A, Hu S, Du G, Lin W, Li L, Bharill S, Ness R, Stecula A, Offer S, Diasio R, Nies A, Schwab M, Cavaletti G, Schlatter E, Ciarimboli G, Schellens J, Isacoff E, Sali A, Chen T, Baker S, Sparreboom A, Pabla N. A phosphotyrosine switch regulates organic cation transporters. Nat Commun 7, 10880, 2016. PMCID4799362
348. Fromme P, Sali A. Editorial overview: Biophysical and molecular biological methods. Curr. Opin. Struct. Biol. 40, ix-xi, 2016.
347. Lasater E, Massi E, Stecula A, Politi J, Tan S, Smith C, Gunthorpe M, Holmes J, Chehab F, Sali A, Shah N. Novel TKI-resistant BCR-ABL1 Gatekeeper Residue Mutations Retain in vitro Sensitivity to Axitinib. Leukemia 30, 1405-9, 2016.
346. Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J. Mol. Biol. 428, 709-19, 2016. PMCID4794384
345. LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J. Biol. Chem. 290, 30390-405, 2015. PMCID4683262
344. Rettenmaier T, Fan H, Karpiak J, Doak A, Sali A, Shoichet B, Wells J. Small-molecule allosteric modulators of the protein kinase PDK1 from structure-based docking. J. Med. Chem. 58, 8285-91, 2015. PMCID5099076
343. Choudhury AR, Sikorska E, van den Boom J, Bayer P, Popenda L, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novič M. Structural model of the Bilitranslocase transmembrane domain supported by NMR and FRET data. PloS One 10, e0135455, 2015. PMCID4546402
342. Smith C, Lin K, Stecula A, Sali A, Shah N. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia 29, 2390-2, 2015. PMCID4675689
341. Reid R, Sgobba M, Raveh B, Rastelli G, Sali A, Santi D. Analytical and simulation-based models for drug release and gel-degradation in a Tetra-PEG hydrogel drug-delivery system. Macromolecules 48, 7359-7369, 2015.
340. Robinson P, Trnka M, Pellarin R, Greenberg C, Bushnell D, Davis R, Burlingame A, Sali A, Kornberg R. Molecular architecture of the yeast Mediator complex. eLife 4, e08719, 2015. PMCID4631838
339. Luo J, Cimermancic P, Viswanath S, Ebmeier C, Kim B, Dehecq M, Raman V, Greenberg C, Pellarin R, Sali A, Taatjes D, Hahn S, Ranish J. Architecture of the human and yeast general transcription and DNA repair factor TFIIH. Mol. Cell 59, 794-806, 2015. PMCID4560838
338. Shi Y, Pellarin R, Fridy P, Fernandez-Martinez J, Thompson M, Li Y, Wang QJ, Sali A, Rout M, Chait B. A strategy for dissecting the architectures of native macromolecular assemblies. Nat Methods 12, 1135-8, 2015. PMCID4803312
337. Carter L, Kim SJ, Schneidman-Duhovny D, Stoehr J, Poncet-Montange G, Weiss T, Tsuruta H, Prusiner S, Sali A. Prion protein-antibody complexes characterized by chromatography-coupled small-angle X-ray scattering. Biophys. J. 109, 793-805, 2015. PMCID4547163
336. Sali A, Berman H, Schwede T, Trewhella J, Kleywegt G, Burley S, Markley J, Nakamura H, Adams P, Bonvin A, Chiu W, Dal Peraro M, Di Maio F, Ferrin T, Grunewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson C, Meiler J, Marti-Renom M, Montelione G, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read R, Saibil H, Schroder G, Schwieters C, Seidel C, Svergun D, Topf M, Ulrich E, Velanker S, Westbrook J. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23, 1156-67, 2015. PMCID4933300
335. Johnson J, Santos S, Pieper U, Sali A, Krogan N, Beltrao P. Prediction of functionally important phospho-regulatory events in Xenopus laevis oocytes. PLOS Comp Bio 11, e1004362, 2015. PMCID4552029
334. Kollman J, Greenberg C, Li S, Moritz M, Zelter A, Fong K, Fernandez J, Sali A, Kilmartin J, Davis T, Agard D. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol 22, 132-137, 2015. PMCID4318760
333. Politis A, Schmidt C, Tjioe E, Sandercock A, Lasker K, Gordiyenko Y, Russel D, Sali A, Robinson C. Topological models of heteromeric protein assemblies from mass spectrometry: Application to the yeast eIF3:eIF5 complex. Chem. Biol. 22, 117-128, 2015. PMCID4306531
332. Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan N. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics 49, 8.19.1-8.19.16, 2015. PMCID4378866
331. Webb B, Sali A. Comparative Protein Structure Modeling Using Modeller. In: Curr Protoc Bioinformatics, 47, pp. 5.6.1-5.6.32, John Wiley and Sons, 2014.
330. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman D, Sali A, Rout M, Chait B. 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
329. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss T, Markina-Inarrairaegui A, Bonanno J, Sauder M, Burley S, Chait BT, Almo S, Rout M, Sali A. 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
328. Medema MH, Cimermancic P, Sali A, Takano E, Fischbach M. A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis. PLoS Comput Biol 10, e1004016, 2014. PMCID4256081
327. Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown L, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach M. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421, 2014. PMCID4123684
326. Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in Integrative Structural Modeling. Curr. Opin. Struct. Biol. 28, 96-104, 2014. PMCID4252396
325. Erzberger J, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett C, Cimermancic P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex. Cell 158, 1125-1135, 2014. PMCID4151992
324. Zeng-Elmore X, Gao X, Pellarin R, Schneidman-Duhovny D, Zhang X, Kozacka K, Tang Y, Sali A, Chalkley R, Cote R, Chu F. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J. Mol. Biol. 426, 3713-3728, 2014. PMCID4253074
323. Street T, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly M, Chu F, Agard D. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J. Mol. Biol. 12, 2393-2404, 2014. PMCID5322795
322. Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait B, Rout M, Dokudovskaya S. Molecular Architecture and Function of the SEA Complex - a Modulator of the TORC1 Pathway. Mol Cell Proteomics 13, 2855-2870, 2014. PMCID4223477
321. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, London N, Branch M, Mashiyama S, Jacobson M, Shoichet B, Babbitt P, Armstrong R, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 6, 1687-1699, 2014. PMCID4068255
320. Spill Y, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. J Synchrotron Radiat 21, 203-208, 2014. PMCID3874021
319. Webb B, Lasker K, Velazquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. 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.
318. Molnar K, Bonomi M, Pellarin R, Clinthorne G, Gonzalez G, Goldberg S, Goulian M, Sali A, DeGrado W. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ. Structure 22, 1239-1251, 2014. PMCID4322757
317. Pieper U, Webb B, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill Y, Weinkam P, Hammel M, Tainer J, Nilges M, Sali A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 42, 336-346, 2014. PMCID3965011
316. Bonomi M, Muller EG, Pellarin R, Kim SJ, Russel D, Ramsden R, Sundin BA, Davis TA, Sali A. Determining protein complex structures based on a Bayesian model of in vivo FRET data. Mol Cell Proteomics 13, 2812-2823, 2014. PMCID4223474
315. Webb B, Sali A. Protein structure modeling with MODELLER. In: Methods in Molecular Biology. Ed: D. Kihara, 1137, pp. 1-15, Springer, New York, 2014.
314. Webb B, Eswar N, Fan H, Khuri N, Pieper U, Dong GQ, Sali A. Comparative Modeling of Drug Target Proteins. In: Chemistry, Molecular Sciences and Chemical Engineering. Ed: J. Reedijk, Elsevier, Waltham, MA, 2014.
313. Berlin K, Castaneda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J. Am. Chem. Soc. 135, 16595-16609, 2013. PMCID3902174
312. Ryan C, Cimermancic P, Szpiechy Z, Sali A, Hernandez R, Krogan N. High-resolution network biology: connecting sequence with function. Nat Rev Genet 14, 865-879, 2013. PMCID4023809
311. Goble A, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet B, Almo S, Swaminathan S, Tanner M, Raushel F. Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes. Biochemistry 52, 6525-6536, 2013. PMCID3813303
310. Kostic M, Lima C, Sali A. Celebrating 20 Years of Structural Biology. Structure 21, 1477-1478, 2013. PMCID TBD by Journal.
309. Martinez-Jimenez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Comp Biol 9, e1003253, 2013. PMCID3789770
308. Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. Optimized atomic statistical potentials: Assessment of protein interfaces and loops. Bioinformatics 29, 3158-3166, 2013. PMCID3842762
307. Weinkam P, Sali A. Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations. J Phys Chem B 117, 13058-13068, 2013. PMCID3973026
306. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt P, Xia Y, Allen K. The consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci USA 110, 3381-3387, 2013. PMCID3767544
305. Hitchcock D, Fan H, Kim J, Vetting M, Hillerich B, Seidel R, Almo S, Shoichet B, Sali A, Raushel F. Structure-guided Discovery of New Deaminase Enzymes. J. Am. Chem. Soc. 135, 13927-13933, 2013. PMCID38227683
304. Schneidman-Duhovny D, Hammel M, Tainer J, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys. J. 105, 962-974, 2013. PMCID3752106
303. Trewhella J, Hendrickson W, Kleywegt G, Sali A, Sato M, Schwede T, Svergun D, Tainer J, Westbrook J, Berman H. 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
302. Schlessinger A, Yee SW, Sali A, Giacomini K. SLC classification: an update. Clin. Pharmacol. Ther. 94, 19-23, 2013. PMCID4068830
301. Geier E, Schlessinger A, Fan H, Gable J, Irwin J, Sali A, Giacomini K. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci USA 110, 5480-5485, 2013. PMCID3619328
300. Ward A, Sali A, Wilson I. Integrative structural biology. Science 339, 913-915, 2013. PMCID3633482
299. Weinkam P, Chen YC, Pons J, Sali A. Impact of mutations on the allosteric conformational equilibrium. J. Mol. Biol. 425, 647-661, 2013. PMCID3557769
298. Guttman M, Weinkam P, Sali A, Lee K. All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins. Structure 21, 321-331, 2013. PMCID3840220
297. Waight A, Pedersen B, Schlessinger A, Bonomi M, Chau B, Roe-Zurz Z, Risenmay A, Sali A, Stroud R. Structural basis for alternating access of a Eukaryotic Calcium/Proton exchanger. Nature 499, 107-110, 2013. PMCID3702627
296. van Dam T, Townsend M, Turk M, Schlessinger A, Sali A, Field M, Huynen M. Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proc Natl Acad Sci USA 110, 6943-6948, 2013. PMCID3637775
295. Schlessinger A, Khuri N, Giacomini K, Sali A. Molecular modeling and ligand docking for Solute Carrier (SLC) transporters. Curr Top Med Chem 13, 843-856, 2013. PMCID4056341
294. Pedersen B, Kumar H, Waight A, Risenmay A, Roe-Zurz Z, Chau B, Schlessinger A, Bonomi M, Harries W, Sali A, Johri A, Stroud R. Crystal structure of a eukaryotic phosphate transporter. Nature 496, 533-536, 2013. PMCID3678552
293. Gradisar H, Bozic S, Doles T, Vengust D, Hafner-Bratkovic I, Mertelj A, Webb B, Sali A, Klavzar S, Jerala R. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nat Chem Biol 9, 362-366, 2013. PMCID3661711
292. Sampathkumar P, Kim SJ, Upla P, Rice W, Phillips J, Timney B, Pieper U, Bonanno J, Fernandez-Martinez J, Hakhverdyan Z, Ketaren N, Matsui T, Weiss R, Stokes D, Sauder JM, Burley S, Sali A, Rout M, Almo S. Structure, dynamics, evolution and function of a major scaffold component in the Nuclear Pore Complex. Structure 21, 560-571, 2013. PMCID3755625
291. Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont M, Fox B, Fromme P, Hendrickson W, Malkowski M, Rees D, Stokes D, Stowell MHB, Wiener M, Rost B, Stroud R, Stevens R, Sali A. Coordinating the impact of structural genomics on the human a-helical transmembrane proteome. Nat Struct Mol Biol 20, 135-138, 2013. PMCID3645303
290. Wittwer MB, Zur AA, Khuri N, Kido Y, Kosaka A, Zhang X, Morrissey KM, Sali A, Huang Y, Giacomini KM. 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
289. Fan H, Hitchcock D, Seidel R, Hillerich B, Lin H, Almo S, Sali A, Shoichet B, Raushel F. 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
288. Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski M, Case D, Chazin W, Cross T, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay L, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil R, HO C, Rule G, Gronenborn A, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue E, Mott H, Nietlispach D, Barsukiv I, Lian L, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis I, Watts A, Conte M, Mason J, Pfuhl M, Sanderson M, Craven J, Williamson M, Dominguez C, Roberts G, Gunther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw D, Steinbeck C, Vendruscolo M, Vuister G, Walters K, Weinstein H, Wuthrich K, Yodoyama S. In support of the BMRB. Nat Struct Mol Biol 19, 854-860, 2012. PMCID TBD by Journal
287. Schneidman-Duhovny D, Kim SJ, Sali A. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12, 17, 2012. PMCID3427135
286. Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini K, Sali A. 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
285. Kolb P, Phan K, Gao Z, Marko A, Sali A, Jacobson KA. Limits of ligand selectivity from docking to models: In silico screening for A1 adenosine receptor antagonists. PLoS One 7, e49910, 2012. PMCID3503826
284. Velazquez-Muriel JA, Lasker K, Russel D, Phillips J, Webb B, Schneidman-Duhovny D, Sali A. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proc Natl Acad Sci USA 109, 18821-18826, 2012. PMCID3503186
283. Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst J, Habelitz S. Self-assembly of Filamentous Amelogenin Requires Calcium and Phosphate: From Dimers via Nanoribbons to Fibrils. Biomacromolecules 13, 3494-3502, 2012. PMCID3496023
282. Trinidad J, Barkan D, Gulledge B, Thalhammer A, Sali A, Schoepfer R, Burlingame A. Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse. Mol Cell Proteomics 11, 215-229, 2012. PMCID3412957
281. Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JDB. Strategic protein target analysis for developing drugs to stop dental caries. Adv. Dent. Res. 22, 86-93, 2012. PMCID3420364
280. Braberg H, Webb B, Tjioe E, Pieper U, Sali A, Madhusudhan MS. SALIGN: A webserver for alignment of multiple protein sequences and structures. Bioinformatics 15, 2072-2073, 2012. PMCID3400954
279. Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P. Shining Light into Black Boxes. Science 336, 159-160, 2012. PMCID4203337
278. Puizdar V, Zajc T, Zerovnik E, Renko M, Pieper U, Eswar N, Sali A, Dolenc I, Turk V. 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
277. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velazquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dotsch V, Raipal A, Pons J, Agard DA, Cheng Y, Sali A. A Method for Integrative Structure Determination of Protein-Protein Complexes. Bioinformatics 28, 3282-3289, 2012. PMCID3519461
276. Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N, Chiu E, Blain K, Esquivies L, Kwon H, Balana B, Pieper U, Sali A, Slesinger P, Kwiatkowski W, Rick R, Choe S. Facile Backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods 8, 834-839, 2012. PMCID3723349
275. Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke J, Matsui T, Tsuruta H, Atwell S, Thompson D, Emtage JS, Wasserman S, Rout M, Sali A, Sauder JM, Almo SC, Burley SK. 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
274. Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109, 1380-1387, 2012. PMCID3277140
273. Pathare G, Nagy I, Bohn S, Unverdorben P, Hubert A, Korner R, Nickell S, Lasker K, Sali A, Tamura T, Nishioka T, Forster F, Baumeister W, Bracher A. 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
272. Russel D, Lasker K, Webb B, Velazquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol 10, e1001244, 2012. PMCID3260315
271. Weinkam P, Pons J, Sali A. Structure-based Model of Allostery Predicts Coupling Between Distant Sites. Proc Natl Acad Sci USA 109, 4875-4880, 2012. PMCID3324024
270. Henderson R, Sali A, Baker M, Carragher B, Devkota B, Downing K, Egelman E, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke S, Medalia O, Penczek P, Rosenthal P, Rossmann M, Schmid M, Schroder G, Steven A, Stokes D, Westbrook J, Wriggers W, Yang H, Young J, Berman H, Chiu W, Kleywegt G, Lawson C. Outcome of the First Electron Microscopy Validation Task Force Meeting. Structure 20, 205-214, 2012. PMCID3328769
269. Fernandez-Martinez J, Phillips J, Sekedat M, Diaz-Avalos R, Velazquez-Muriel J, Franke J, Williams R, Stokes D, Chait B, Sali A, Rout M. Structure-function Map for a Heptameric Component of the Nuclear Pore Complex. J. Cell Biol. 196, 419-434, 2012. PMCID3283990
268. Fan H, Irwin J, Sali A. Virtual Ligand Screening Against Comparative Protein Structure Models. Methods Mol. Biol. 819, 105-126, 2012. PMCID3386294
267. Lasker K, Velazquez-Muriel J, Webb B, Yang Z, Ferrin TE, Sali A. 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.
266. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang C, Pettersen E, Goddard T, Meng E, Sali A, Ferrin T. UCSF Chimera, MODELLER, and IMP: an integrated Modeling System. J. Struct. Biol. 179, 269-278, 2012. PMCID3410985
265. Gerlt J, Allen K, Almo S, Armstrong R, Babbitt P, Cronan J, Dunaway-Mariano D, Imker H, Jacobson M, Minor W, Poulter C, Raushel F, Sali A, Shoichet B, Sweedler J. The Enzyme Function Initiative. Biochemistry 50, 9950-9962, 2011. PMCID3238057
264. Goble AM, Fan H, Sali A, Raushel FM. Discovery of a Cytokinin Deaminase. ACS Chem Biol 6, 1036-1040, 2011. PMCID3199332
263. Choi J, Yee S, Ramirez A, Morrissey K, Jang G, Joski P, Mefford J, Hesselson S, Schlessinger A, Jenkins G, Castro R, Johns S, Stryke D, Sali A, Ferrin T, Witte J, Kwok P, Roden D, Wilke R, McCarty C, Davis R, Giacomini K. A Common Promoter Variant in MATE2-K Is Associated with Poor Response to Metformin. Clin. Pharmacol. Ther. 90, 674-684, 2011. PMCID3329222
262. Schlessinger A, Geier E, Fan H, Irwin J, Shoichet B, Giacomini K, Sali A. Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET. Proc Natl Acad Sci USA 108, 15810-15815, 2011. PMCID3179104
261. Carlsson J, Coleman R, Setola V, Irwin J, Fan H, Schlessinger A, Sali A, Roth B, Shoichet B. 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
260. Tjioe E, Lasker K, Webb B, Wolfson H, Sali A. MultiFit: A web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res 39, 167-170, 2011. PMCID3125811
259. Jager S, Kim DY, Shindo K, Kwon E, LaRue R, Mahon C, Cimermancic P, Yen L, Stanley D, Li M, Burlingame A, Sali A, Craik C, Harris R, Gross J, Krogan N. Vif Hijacks CBFβ to Degrade APOBEC3G and Promote HIV-1 Infection. Nature 481, 371-375, 2011. PMCID3310910
258. Jager S, Cimermancic P, Gulbahce N, Johnson J, McGovern K, Clarke S, Shales M, Mercenne G, Li K, Barry H, Jang G, Akiva E, Pache L, Marlett J, Roth S, Stephens M, D’Orso I, Fernandes J, Fahey M, Mahon C, O’Donoghue A, Todorovic A, Morris J, Maltby D, Alber T, Cagney G, Bushman F, Young J, Chanda S, Sundquist W, Kortemme T, Hernandez R, Craik C, Burlingame A, Sali A, Frankel A, Krogan N. Global Landscape of HIV-Human Protein Complexes. Nature 481, 365-370, 2011. PMCID3310911
257. Fan H, Schneidman D, Irwin JJ, Dong G, Shoichet B, Sali A. Statistical Potential for Modeling and Ranking Protein-Ligand Interactions. J Chem Inf Model 51, 3078-3092, 2011. PMCID3246566
256. Field M, Sali A, Rout M. On a bender: Bars, ESCRTs, COPs, and finally getting your coat. J. Cell Biol. 193, 963-972, 2011. PMCID3115789
255. Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MC, Dargemont C. 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
254. Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. J. Am. Chem. Soc. 133, 2080-2083, 2011. PMCID3043370
253. Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, S.J. Kim, Phillips J, Pieper U, Fernandez-Martinez J, Franke J, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK. 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
252. Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velazquez-Muriel J, Russel D, Sali A. 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.
251. Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM. Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase. Biochemistry 50, 1917-1927, 2011. PMCID3059353
250. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjolander K, Ferrin TE, Burley SK, Sali A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39, 465-474, 2011. PMCID3013688
249. Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. 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.
248. Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J. Struct. Biol. 3, 461-471, 2011. PMCID3040266
247. Forster F, Lasker K, Nickell S, Sali A, Baumeister W. Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics 9, 1666-1677, 2010. PMCID2938054
246. Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional Hot Spots in Human ATP-binding Cassette Transporter Nucleotide Binding Domains. Protein Sci. 19, 2110-2121, 2010. PMCID3005782
245. Chen L, Takizawa M, Chen E, Schlessinger A, Choi JH, Segenthelar J, Sali A, Kubo M, Nakamura S, Iwamoto Y, Iwasaki N, Giacomini KM. 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
244. Lasker K, Sali A, Wolfson HJ. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins:Struct Funct Bioinform 78, 3205-3211, 2010. PMCID2952722
243. Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn K, Bonanno J, Pieper U, Fajardo JE, Fiser A, Almo S, Swaminathan A, Chance M, Baker D, Atwell S, Thompson D, Emtage JS, Wasserman S, Sali A, Sauder JM, Burley S. 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
242. Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup 145. Proteins:Struct Funct Bioinform 78, 1992-1998, 2010. PMCID3136511
241. Lasker K, Phillips JL, Russel D, Velazquez-Muriel J, Schneidman-Duhovny D, Webb B, Schlessinger A, Sali A. Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data. Mol Cell Proteomics 9, 1689-1702, 2010. PMCID2938050
240. Schneidman-Duhovny D, Hammel M, Sali A. FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles. Nucleic Acids Res 38, 541-544, 2010. PMCID2896111
239. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. Comparison of Human Solute Carriers. Protein Sci. 19, 412-428, 2010. PMCID2866268
238. Chen L, Pawlikowski B, Schlessinger A, More S, Stryke D, Johns SJ, Portman M, Ferrin TE, Sali A, Giacomini K. Role of organic cation transporter 3 (SLC22A3) and Its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics 20, 687-699, 2010. PMCID2976715
237. Gruswitz F, Chaudhary S, Ho J, Schlessinger A, Bobak P, Ho C, Sali A, Westhoff C, Stroud R. 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
236. Barkan D, Hostetter D, Mahrus S, Pieper U, Wells J, Craik C, Sali A. Prediction of Protease Substrates using Sequence and Structure Features. Bioinformatics 26, 1714-1722, 2010. PMCID2894511
235. Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comp Biol 6, e1000668, 2010. PMCID2816688
234. Kroetz D, Ahituv N, Burchard E, Guo S, Sali A, Giacomini K. 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
233. Forster F, Lasker K, Beck F, Nickell S, Sali A, Baumeister W. An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem. Biophys. Res. Commun. 388, 228-233, 2009. PMCID2771176
232. Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet B, Sali A. Molecular Docking Screens Using Comparative Models of Proteins. J Chem Inf Model 49, 2512-2527, 2009. PMCID2790034
231. Taylor DJ, Devkota B, Huang AD, Topf M, Eswar N, Sali A, Harvey SC, Frank J. Comprehensive Molecular Structure of the Eukaryotic Ribosome. Structure 17, 1591-1604, 2009. PMCID2814252
230. Lezon T, Sali A, Bahar I. Global motions of the nuclear pore complex:Insights from Elastic Network Models. PLoS Comp Biol 5, e1000496, 2009. PMCID2725293
229. Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz D, Giacomini KM, Stroud RM, Sali A. A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics 10, 269-280, 2009. PMCID2780624
228. DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT. The Establishment of Nuclear Pore Complex Architecture Occurred Early in Evolution. Mol Cell Proteomics 8, 2119-2130, 2009. PMCID2742445
227. Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel 22, 569-574, 2009. PMCID2909824
226. Lasker K, Topf M, Sali A, Wolfson HJ. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J. Mol. Biol. 388, 180-194, 2009. PMCID2680734
225. Nickell S, Beck F, Scheres SHW, Korinek A, Forster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko J, Carazo J-M, Mann M, Baumeister W. Insights into the Molecular Architecture of the 26S Proteasome. Proc. Natl. Acad. Sci. U. S. A. 29, 11943-11947, 2009. PMCID2715492
224. Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. ModLink+: Improving fold recognition by using protein-protein interactions. Bioinformatics 25, 1506-1512, 2009. PMCID2687990
223. Orti L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. A kernel for the Tropical Disease Initiative. Nat. Biotechnol. 27, 320-321, 2009. PMCID3088649
222. Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W. 2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins. J. Struct. Funct. Genom. 10, 193-208, 2009. PMCID2705707
221. Pandey KC, Barkan DT, Sali A, Rosenthal PJ. Regulatory elements within the prodomain of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. PLoS One 4(5):e5694, 2009. PMCID2682653
220. Orti L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis 3, e418, 2009. PMCID2667270
219. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure 17, 151-159, 2009. PMCID2739730
218. Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velazquez-Muriel JA, Sali A. The structural dynamics of macromolecular processes. Curr. Opin. Cell Biol. 21, 97-108, 2009. PMCID2774249
217. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci. 18, 1306-1315, 2009. PMCID2774440
216. Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD 3rd, Miercke LJ, Giacomini KM, Sali A, Stroud RM. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J. Mol. Biol. 385, 820-830, 2009. PMCID2659619
215. Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM. Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. J. Struct. Funct. Genom. 10, 9-16, 2009. PMCID2756966
214. Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 37, D347-354, 2009. PMCID2686492
213. Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J. Struct. Funct. Genom. 10, 107-125, 2009. PMCID2693957
212. Eswar N, Sali A. 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.
211. Graslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park H, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim S, Rao Z, Shi Y, Terwilliger TC, Kim C, Hung L, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schutz A, Heinemann U, Yokoyama S, Bussow K, Gunsalus KC. Protein production and purification (vol 5, pg 135, 2008). Nat Methods 5, 369-369, 2008. PMCID3178102
210. Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. 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
209. Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini. Cell 134, 866-876, 2008. PMCID2566540
208. Chiang RA, Sali A, Babbitt PC. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 4, e1000142, 2008. PMCID2453236
207. Anderson CM, Korkin D, Smith DL, Makovets S, Seidel JJ, Sali A, Blackburn EH. Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break. Genes Dev. 22, 854-859, 2008. PMCID2279195
206. Forster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A. Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J. Mol. Biol. 382, 1089-1106, 2008. PMCID2745287
205. Eramian D, Eswar N, Shen MY, Sali A. How well can the accuracy of comparative protein structure models be predicted? Protein Sci. 17, 1881-1893, 2008. PMCID2578807
204. Krukenberg KA, Forster F, Rice LM, Sali A, Agard DA. Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure 16, 755-765, 2008. PMCID2600884
203. Karchin R, Agarwal M, Sali A, Couch F, Beattie MS. Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios. Cancer Inform 6, 203-216, 2008. PMCID2587343
202. Aguero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL. Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov 7, 900-907, 2008. PMCID3184002
201. Espadaler J, Eswar N, Querol E, Aviles FX, Sali A, Marti-Renom MA, Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics 9, 249, 2008. PMCID2430716
200. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 16, 295-307, 2008. PMCID2409374
199. Alber F, Forster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem. 77, 443-477, 2008.
198. Chandramouli P, Topf M, Menetret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure 16, 535-548, 2008. PMCID2775484
197. Alber F, Chait BT, Rout MP, Sali A. 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.
196. Burley SK, Almo SC, Bonanno JB, Chance MR, Emtage S, Fiser A, Sali A, Sauder JM, Swaminathan S. Structure Genomics of Protein Superfamilies. In: Structural Bioinformatics, 2nd Edition. Ed: J. Gu, P.E. Bourne, Wiley-Blackwell, New York, NY, 2008.
195. Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol 15, 746-753, 2008. PMCID2546500
194. Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF. Crystallographic conformers of actin in a biologically active bundle of filaments. J. Mol. Biol. 375, 331-336, 2008. PMCID2680129
193. Schwede T, Sali A, Eswar N, Peitsch MC. Protein Structure Modeling. In: Computational Structural Biology. Ed: T. Schwede, M.C. Peitsch, pp. 3-35, World Scientific Publishing Ltd., Singapore, 2008.
192. Eswar N, Eramian D, Webb B, Shen MY, Sali A. Protein structure modeling with MODELLER. Methods Mol. Biol. 426, 145-159, 2008.
191. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A. Determining the architectures of macromolecular assemblies. Nature 450, 683-694, 2007.
190. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP. The molecular architecture of the nuclear pore complex. Nature 450, 695-701, 2007.
189. Robinson CV, Sali A, Baumeister W. The molecular sociology of the cell. Nature 450, 973-982, 2007.
188. Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology 148, 1059-1079, 2007.
187. Sali A, Lima CD, Kostic M. Structural genomics. Structure 15, 1341, 2007.
186. Melo F, Sali A. Fold assessment for comparative protein structure modeling. Protein Sci. 16, 2412-2426, 2007.
185. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK. Structural genomics of protein phosphatases. J. Struct. Funct. Genom. 8, 121-140, 2007.
184. Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Host pathogen protein interactions predicted by comparative modeling. Protein Sci. 16, 2585-2596, 2007.
183. Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Res 35, W393-397, 2007.
182. Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics 8 Suppl 4, S4, 2007.
181. Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol 3, 1761-1771, 2007.
180. Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol 3, e241, 2007.
179. Soranzo N, Kelly L, Martinian L, Burley MW, Thom M, Sali A, Kroetz DL, Goldstein DB, Sisodiya SM. Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia 48, 674-683, 2007.
178. Feyfant E, Sali A, Fiser A. Modeling mutations in protein structures. Protein Sci. 16, 2030-2041, 2007.
177. Wang SX, Pandey KC, Scharfstein J, Whisstock J, Huang RK, Jacobelli J, Fletterick RJ, Rosenthal PJ, Abrahamson M, Brinen LS, Rossi A, Sali A, McKerrow JH. 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.
176. Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, Baumbach L, Sutphen R, Pickard-Brzosowicz JL, Nathanson KL, Sali A, Goldgar D, Couch FJ, Radice P, Monteiro AN. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res. 67, 1494-1501, 2007.
175. Eswar N, Sali A. 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.
174. Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac. Symp. Biocomput., 51-63, 2007.
173. Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A. Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning. PLoS Comp. Biol. 3, e26, 2007.
172. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Chapter 2, Unit 2.9, 2007.
171. Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 15, 2507-2524, 2006.
170. Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J. Mol. Biol. 363, 835-857, 2006.
169. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL Jr., Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14, 1211-1217, 2006.
168. Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacol. Rev. 58, 1-2, 2006.
167. Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. Protein complex compositions predicted by structural similarity. Nucleic Acids Res 34, 2943-2952, 2006.
166. Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci. 15, 2366-2380, 2006.
165. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Chapter 5, Unit 5.6, 2006.
164. Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP. Protease accessibility laddering: a proteomic tool for probing protein structure. Structure 14, 653-660, 2006.
163. Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. A composite score for predicting errors in protein structure models. Protein Sci. 15, 1653-1666, 2006.
162. Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Comp. Biol. 2, e153, 2006.
161. Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J. Mol. Biol. 357, 1655-1668, 2006.
160. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34, D291-295, 2006.
159. Lima C, Puglisi J, Sali A, Szewczak L. Editorial. Structure 14, 801, 2006.
158. Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. Variable gap penalty for protein sequence-structure alignment. Protein Engineering, Design & Selection 19, 129-133, 2006.
157. Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A. Simple fold composition and modular architecture of the nuclear pore complex. Proc. Natl. Acad. Sci. U. S. A. 103, 2172-2177, 2006.
156. McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nature Structural Molecular Biology 12, 886-892, 2005.
155. Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Curr. Opin. Struct. Biol. 15, 578-585, 2005.
154. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J. Struct. Funct. Genom. 6, 225-232, 2005.
153. Shen MY, Davis FP, Sali A. The optimal size of a globular protein domain: A simple sphere-packing model. Chem Phys Lett 405, 224-228, 2005.
152. Korkin D, Davis FP, Sali A. Localization of protein-binding sites within families of proteins. Protein Sci. 14, 2350-2360, 2005.
151. Sali A, Chiu W. Macromolecular assemblies highlighted. Structure 13, 339-341, 2005.
150. Dvorak J, Delcroix M, Rossi A, Vopalensky V, Pospisek M, Sedinova M, Mikes L, Sajid M, Sali A, Mckerrow JH, Horak P, Caffrey CR. 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.
149. Yasuda S, Morokawa N, Wong GW, Rossi A, Madhusudhan MS, Sali A, Askew YS, Adachi R, Silverman GA, Krilis SA, Stevens RL. Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22. Blood 105, 3893-3901, 2005.
148. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21, 2814-2820, 2005.
147. Davis FP, Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21, 1901-1907, 2005.
146. Alber F, Kim MF, Sali A. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13, 435-445, 2005.
145. Madhusudhan MS, Marti-Renom MA, Eswar N, John B, Pieper U, Karchin R, Shen Min-yi, Sali A. Comparative Protein Structure Modeling. In: Proteomics Protocols Handbook. Ed: J.M. Walker, pp. 831-860, Humana Press Inc., Totowa, NJ, 2005.
144. Karchin R, Kelly L, Sali A. Improving functional annotation of non-synonomous SNPs with information theory. Pac. Symp. Biocomput., 397-408, 2005.
143. Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J. Struct. Biol. 149, 191-203, 2005.
142. Espadaler J, Aragues R, Eswar N, Marti-Renom MA, Querol E, Aviles FX, Sali A, Oliva B. Detecting remotely related proteins by their interactions and sequence similarity. Proc. Natl. Acad. Sci. U. S. A. 102, 7151-7156, 2005.
141. Maurer SM, Rai A, Sali A. Finding Cures for Tropical Diseases: Is Open Source an Answer? PLoS Medicine 1, e56, 2004.
140. Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP. Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2, e380, 2004.
139. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14, 313-324, 2004.
138. Jacobson M, Sali A. 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.
137. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. High-throughput computational and experimental techniques in structural genomics. Genome Res. 14, 2145-2154, 2004.
136. Maurer SM, Rai A, Sali A. 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.
135. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32, D217-D222, 2004.
134. Maurer SM, Rai A, Sali A. Finding Cures for Tropical Diseases: Is Open Source An Answer? Minnesota Journal of Law, Science & Technology 6, 169-175, 2004.
133. John B, Sali A. Detection of homologous proteins by an intermediate sequence search. Protein Sci. 13, 54-62, 2004.
132. Alber F, Eswar N, Sali A. Structure determination of macromolecular complexes by experiment and computation. Practical Bioinformatics, Ed: J.Bujnicki 15, 73-96, 2004.
131. Marti-Renom MA, Madhusudhan MS, Sali A. Alignment of protein sequences by their profiles. Protein Sci. 13, 1071-1087, 2004.
130. Rossi A, Deveraux Q, Turk B, Sali A. Comprehensive search for cysteine cathepsins in the human genome. Biol. Chem. 385, 363-372, 2004.
129. Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res. 64, 3790-3797, 2004.
128. Fiser A, Sali A. ModLoop: automated modeling of loops in protein structures. Bioinformatics 19, 2500-2501, 2003.
127. Sali A. NIH workshop on structural proteomics of biological complexes. Structure 11, 1043-1047, 2003.
126. Marti-Renom MA, Fiser A, Madhusudhan MS, John B, Stuart AC, Eswar N, Pieper U, Shen M-Y, Sali A. 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.
125. Lee SA, Shen EL, Fiser A, Sali A, Guo S. The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons. Development 130, 2669-2679, 2003.
124. Gao HX, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J. Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement. Cell 113, 789-801, 2003.
123. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res 31, 3375-3380, 2003.
122. John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 31, 3982-3992, 2003.
121. Koh IYY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Grana O, Pazos F, Valencia A, Sali A, Rost B. EVA: evaluation of protein structure prediction servers. Nucleic Acids Res 31, 3311-3315, 2003.
120. Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics. Nature 422, 216-225, 2003.
119. Fiser A, Sali A. Comparative Protein Structure Modeling. In: Protein Structure. Ed: D. Chasman, pp. 167-206, Marcel Dekker, Inc., 2003.
118. Marti-Renom MA, Yerkovich B, Sali A. 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.
117. Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics 19, 165-166, 2003.
116. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374, 461-491, 2003.
115. Iverson GM, Reddel S, Victoria EJ, Cockerill KA, Wang YX, Marti-Renom MA, Sali A, Marquis DM, Krilis SA, Linnik MD. 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.
114. Marti-Renom MA, Yerkovich B, Sali A. Comparative protein structure prediction. In: Current Protocols in Protein Science, pp. 2.9.1-2.9.22, John Wiley & Sons, 2002.
113. Yang Y, Li LX, Wong GW, Krilis SA, Madhusudhan MS, Sali A, Stevens RL. 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.
112. Rajashankar KR, Chance MR, Burley SK, Jiang J, Almo SC, Bresnick AR, Dodatko T, Huang R, He G, Chen H, Sullivan M, Toomey J, Thirumuruhan RA, Franklin WA, Sali A, Pieper U, Eswar N, Ilyin V, McMahan L. Structural Genomics at the National Synchrotron Light Source. NSLS Activity Report 2001 2, 28-32, 2002.
111. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He GS, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. Structural genomics: A pipeline for providing structures for the biologist. Protein Sci. 11, 723-738, 2002.
110. Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res 30, 255-259, 2002.
109. Fiser A, Feig M, Brooks CL, Sali A. Evolution and physics in comparative protein structure modeling. Acc. Chem. Res. 35, 413-421, 2002.
108. Sali A, Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B. Reply to Moult et al. Structure 10, 292-293, 2002.
107. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure 10, 435-440, 2002.
106. Stuart AC, Ilyin VA, Sali A. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18, 200-201, 2002.
105. Melo F, Sanchez R, Sali A. Statistical potentials for fold assessment. Protein Sci. 11, 430-448, 2002.
104. Vernal J, Fiser A, Sali A, Muller M, Cazzulo JJ, Nowicki C. Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis. Biochem. Biophys. Res. Commun. 293, 633-639, 2002.
103. Baker D, Sali A. Protein structure prediction and structural genomics. Science 294, 93-96, 2001.
102. Groft CM, Beckmann R, Sali A, Burley SK. Response to Paoli. Nat. Struct. Biol. 8, 745, 2001.
101. Borodovsky M, Koonin E, Burge C, Fickett J, Logsdon J, Sali A, Stormo G, Zhulin I. 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.
100. Wong GW, Yasuda S, Madhusudhan MS, Li L, Yang Y, Krilis SA, Sali A, Stevens RL. 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.
99. Beckmann R, Spahn CMT, Eswar N, Helmers J, Penczek PA, Sali A, Frank J, Blobel G. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361-372, 2001.
98. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell 107, 373-386, 2001.
97. Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc. Natl. Acad. Sci. U. S. A. 98, 12896-12901, 2001.
96. Sali A. Target practice. Nat. Struct. Biol. 8, 482-484, 2001.
95. Barrientos LG, Campos-Olivas R, Louis JM, Fiser A, Sali A, Gronenborn AM. 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.
94. Wong GW, Li L, Madhusudhan MS, Krilis SA, Gurish MF, Rothenberg ME, Sali A, Stevens RL. Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases. J. Biol. Chem. 276, 20648-20658, 2001.
93. Marti-Renom MA, Ilyin VA, Sali A. DBAli: a database of protein structure alignments. Bioinformatics 17, 746-747, 2001.
92. Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17, 1242-1243, 2001.
91. Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat. Genet. 27, 337-340, 2001.
90. Groft CM, Beckmann R, Sali A, Burley SK. Crystal structures of ribosome anti-association factor IF6. Nat. Struct. Biol. 7, 1156-1164, 2000.
89. Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling. In: Computational Biochemistry and Biophysics. Ed: M. Watanabe, B. Roux, A. Mackerell, O. Becker, pp. 275-312, Marcel Dekker, 2000.
88. Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, Madhusudhan MS, Mirkovic N, Sali A. Protein structure modeling for structural genomics. Nat. Struct. Biol. 7, 986-990, 2000.
87. Jin SK, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine AJ. Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A. 97, 7301-7306, 2000.
86. Liedtke W, Choe Y, Marti-Renom MA, Bell AM, Denis CS, Sali A, Hudspeth AJ, Friedman JM, Heller S. Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor. Cell 103, 525-535, 2000.
85. Fiser A, Do RKG, Sali A. Modeling of loops in protein structures. Protein Sci. 9, 1753-1773, 2000.
84. Wu G, McArthur AG, Fiser A, Sali A, Sogin ML, Muller M. Core histones of the amitochondriate protist, Giardia lamblia. Mol. Biol. Evol. 17, 1156-1163, 2000.
83. Sanchez R, Sali A. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol. Biol. 143, 97-129, 2000.
82. Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25, 331-339, 2000.
81. Sanchez R, Pieper U, Mirkovic N, de Bakker PIW, Wittenstein E, Sali A. ModBase, a database of annotated comparative protein structure models. Nucleic Acids Res 28, 250-253, 2000.
80. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
79. Huang C, Morales G, Vagi A, Chanasyk K, Ferrazzi M, Burklow C, Qiu WT, Feyfant E, Sali A, Stevens RL. 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.
78. Baldi P, Borodovsky M, Brunak S, Burge C, Fickett J, Henikoff S, Koonin E, Sali A, Sander C, Stormo G. The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function. Bioinformatics 15, 865-866, 1999.
77. Sali A. Functional links between proteins. Nature 402, 23, 25-26, 1999.
76. Sali A, Kuriyan J. Challenges at the frontiers of structural biology (Reprinted from Trends in Biochemical Science, vol 12, Dec., 1999). Trends Cell Biol. 9, M20-M24, 1999.
75. Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T, Lin D, Sali A, Studier FW, Swaminathan S. Structural genomics: beyond the human genome project. Nat. Genet. 23, 151-157, 1999.
74. Wong GW, Tang Y, Feyfant E, Sali A, Li L, Li Y, Huang C, Friend DS, Krilis SA, Stevens RL. 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.
73. Miwa JM, Ibanez-Tallon I, Crabtree GW, Sanchez R, Sali A, Role LW, Heintz N. lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS. Neuron 23, 105-114, 1999.
72. Nagata T, Gupta V, Sorce D, Kim WY, Sali A, Chait BT, Shigesada K, Ito Y, Werner MH. Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain. Nat. Struct. Biol. 6, 615-619, 1999.
71. Wu G, Fiser A, ter Kuile B, Sali A, Muller M. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proc. Natl. Acad. Sci. U. S. A. 96, 6285-6290, 1999.
70. Sanchez R, Sali A. Comparative protein structure modeling in genomics. Journal of Computational Physics 151, 388-401, 1999.
69. Sanchez R, Sali A. MODBASE: A database of comparative protein structure models. Bioinformatics 15, 1060-1061, 1999.
68. Sali A. 100,000 protein structures for the biologist. Nat. Struct. Biol. 5, 1029-1032, 1998.
67. Sanchez R, Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. U. S. A. 95, 13597-13602, 1998.
66. Wolf E, Vassilev A, Makino Y, Sali A, Nakatani Y, Burley SK. Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell 94, 439-449, 1998.
65. Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich E. Temperature dependence of the folding rate in a simple protein model: Search for a glass transition. J. Chem. Phys. 108, 6466-6483, 1998.
64. Kandiah DA, Sali A, Sheng Y, Victoria EJ, Marquis DM, Coutts SM, Krilis SA. Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects. Advanced Immunology Journal 70, 507-563, 1998.
63. Huang C, Sali A, Stevens RL. Regulation and function of mast cell proteases in inflammation. J. Clin. Immunol. 18, 169-183, 1998.
62. Dobson CM, Sali A, Karplus M. Protein folding: A perspective from theory and experiment. Angewandte Chemie Int Ed 37, 868-893, 1998.
61. Sheng Y, Krilis SA, Sali A. 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.
60. Sanchez R, Badretdinov AYa, Feyfant E, Sali A. Homology protein structure modeling. Transactions of the American Crystallographic Association 32, 81-91, 1997.
59. Guenther B, Onrust R, Sali A, O'Donnell M, Kuriyan J. Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91, 335-345, 1997.
58. Sanchez R, Sali A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins Suppl 1, 50-58, 1997.
57. Hunt JE, Friend DS, Gurish MF, Feyfant E, Sali A, Huang C, Ghildyal N, Stechschulte S, Austen KF, Stevens RL. 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.
56. Koulich D, Orlova M, Malhotra A, Sali A, Darst SA, Borukhov S. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J. Biol. Chem. 272, 7201-7210, 1997.
55. Sanchez R, Sali A. Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7, 206-214, 1997.
54. Sanchez R, Sali A. Comparative protein modeling as an optimization problem. Journal of Molecular Structure (Theochem) 398, 489-496, 1997.
53. Huang C, Wong GW, Ghildyal N, Gurish MF, Sali A, Matsumoto R, Qiu WT, Stevens RL. 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.
52. Russel M, Linderoth NA, Sali A. Filamentous phage assembly: variation on a protein export theme. Gene 192, 23-32, 1997.
51. Wu S, de Lencastre H, Sali A, Tomasz A. A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing. Microb. Drug Resist. 2, 277-286, 1996.
50. Dinner AR, Sali A, Karplus M. The folding mechanism of larger model proteins: role of native structure. Proc. Natl. Acad. Sci. U. S. A. 93, 8356-8361, 1996.
49. Xu LZ, Sanchez R, Sali A, Heintz N. Ligand specificity of brain lipid-binding protein. J. Biol. Chem. 271, 24711-24719, 1996.
48. Ghildyal N, Friend DS, Stevens RL, Austen KF, Huang C, Penrose JF, Sali A, Gurish MF. 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.
47. Sheng Y, Sali A, Herzog H, Lahnstein J, Krilis SA. 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.
46. Karplus M, Sali A, Shakhnovich E. Kinetics of protein folding. Nature 373, 664-665, 1995.
45. Sali A. Modeling mutations and homologous proteins. Curr. Opin. Biotechnol. 6, 437-451, 1995.
44. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins 23, 318-326, 1995.
43. Sali A, Shakhnovich E, Karplus M. 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.
42. Sali A, Shakhnovich E, Karplus M. 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.
41. Sali A. Comparative protein modeling by satisfaction of spatial restraints. Mol. Med. Today 1, 270-277, 1995.
40. Matsumoto R, Sali A, Ghildyal N, Karplus M, Stevens RL. 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.
39. Wu XD, Knudsen B, Feller SM, Zheng J, Sali A, Cowburn D, Hanafusa H, Kuriyan J. 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.
38. Sali A. MODELLER: Implementing 3D protein modeling. In: mc^2, 2, pp. 5, Molecular Simulations Inc., 1995.
37. Karplus M, Caflisch A, Sali A, Shakhnovich E. 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.
36. Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5, 58-73, 1995.
35. Dinner A, Sali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations. J. Chem. Phys. 101, 1444-1451, 1994.
34. Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature 369, 248-251, 1994.
33. Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235, 1614-1636, 1994.
32. Sali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3, 1582-1596, 1994.
31. Sali A, Blundell T. 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.
30. Sali A, Matsumoto R, McNeil HP, Karplus M, Stevens RL. 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.
29. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
28. Overington JP, Zhu ZY, Sali A, Johnson MS, Sowdhamini R, Louie GV, Blundell TL. Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins. Biochem. Soc. Trans. 21 ( Pt 3), 597-604, 1993.
27. Johnson MS, Overington JP, Sali A, Blundell TL. 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.
26. Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci. 1, 216-226, 1992.
25. Zhu ZY, Sali A, Blundell TL. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng. 5, 43-51, 1992.
24. Veerapandian B, Cooper JB, Sali A, Blundell TL, Rosati RL, Dominy BW, Damon DB, Hoover DJ. Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases. Protein Sci. 1, 322-328, 1992. PMC2142209
23. Sali A, Veerapandian B, Cooper JB, Moss DS, Hofmann T, Blundell TL. Domain flexibility in aspartic proteinases. Proteins 12, 158-170, 1992.
22. Sali A, Overington JP, Johnson MS, Blundell TL. 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.
21. Blundell TL, Cooper JB, Donnelly D, Driessen H, Edwards Y, Eisenmenger F, Frazao C, Johnson M, Niefind K, Newman M, Overington J, Sali A, Slingsby C, Nalini V, Zhu ZY. 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.
20. Blundell TL, Cooper JB, Sali A, Zhu ZY. Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases. Adv. Exp. Med. Biol. 306, 443-453, 1991.
19. Blundell TL, Johnson MS, Overington JP, Sali A. 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.
18. Johnson MS, Overington J, Sali A, Zhu Z, Donnelly D, Thomas P, McLeod A, Goold R, Topham C, Blundell TL. From comparative structure analysis to protein engineering: Knowledge-based protein modelling and design. Fresenius Journal of Analytic Chemistry 337, 1-3, 1990.
17. Johnson MS, Overington JP, Sali A. 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.
16. Johnson MS, Sali A, Blundell TL. Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol. 183, 670-690, 1990.
15. Overington JP, Johnson MS, Topham C, McLeod A, Sali A, Zhu ZY, Sibanda L, Blundell TL. Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure. Curr. Sci. 59, 867-874, 1990.
14. Overington J, Johnson MS, Sali A, Blundell TL. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Procedures in Biological Science 241, 132-145, 1990.
13. Veerapandian B, Cooper JB, Sali A, Blundell TL. 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.
12. Sali A, Overington JP, Johnson MS, Blundell TL. From Comparisons of protein sequences and structures to protein modelling and design. Trends Biochem. Sci. 15, 235-240, 1990.
11. Sali A, Blundell TL. 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.
10. Blundell TL, Carney D, Hubbard T, Johnson MS, McLeod A, Overington JP, Sali A, Sutcliffe MS, Thomas P. 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.
9. Blundell TL, Elliott G, Gardner SP, Hubbard T, Islam S, Johnson M, Mantafounis D, Murrayrust P, Overington J, Pitts JE, Sali A, Sibanda BL, Singh J, Sternberg MJE, Sutcliffe MJ, Thornton JM, Travers P. Protein engineering and design. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 324, 447-460, 1989.
8. Sali A, Veerapandian B, Cooper JB, Foundling SI, Hoover DJ, Blundell TL. 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.
7. Turk V, Jerala R, Lenarcic B, Sali A. 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.
6. Lah T, Kregar I, Sali A, Lenarcic B, Kotnik M, Kostka V, Turk V. Circular dichroism studies of different aspartyl proteinases and their interactions with pepstatin. Periodicum Biologorum 90, 31-38, 1988.
5. Sali A, Turk V. 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.
4. Kotnik M, Sali A, Kos J, Turk B, Turk V. 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.
3. Turk V, Brzin J, Lenarcic B, Sali A, Machleidt W. 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.
2. Lenarcic B, Ritonja A, Sali A, Kotnik M, Turk V, Machleidt W. 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.
1. Renko M, Sali A, Turk V, Pokomy M, Kregar I. A neutral metalloproteinase from Streptomyces rimosus. Vestnik Slovenskega Kemijskega Drustva 32/2, 161-173, 1985.