Publications
370. Webb B, Sali A. Protein structure modeling with MODELLER. In: Methods in Molecular Biology, in press.

369. 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). submitted.

368. Fromme P, Sali A. Editorial overview: Biophysical and molecular biological methods. Curr. Opin. Struct. Biol. 40, ix-xi, 2016.

367. 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. submitted.

366. 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.

365. 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.

364. Chen A, Vieth M, Timm D, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Lu J, Liu L. Reconstruction of 3D Conformations of cMET Antibodies from EM 2D Class Averages. submitted.

363. 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. Integrative mapping of enzymatic pathways. submitted.

362. Wang X, Cimermancic P, Yu C, Sakata E, Guo X, Greenberg C, Schweitzer A, Huszagh AS, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Dixon J, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. submitted.

361. Winter MB, La Greca F, Cimermancic P, Buchholz TJ, Anderl JL, Arastu-Kapur S, Sali A, O’Donoghue AJ, Craik CS. Distinguishing the Human Immuno- and Constitutive Proteasomes with Global Substrate Specificity Profiling. submitted.

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 [Epub ahead of print], 2016.

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, in press.

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.

354. 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. A cross-activating c-Met/β1 integrin complex drives therapeutic resistance. submitted.

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. 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. submitted.

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.

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.

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.

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 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.

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.

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.

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.