Publications
243. 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, in press.
242. Korkin D, Chiu W, Frydman J, Sali A. Configuration of paralogous subunits in protein assemblies. submitted.
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. submitted.
240. Schneidman-Duhovny D, Hammel A, Sali A. FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles. submitted.
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. PMCID TBD by Journal
238. 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. PMCID TBD by Journal
237. Chen L, Pawlikowski B, Schlessinger A, More S, Sali A, Giacomini K. Metformin Transport by the Organic Cation Transporter OCT3, (SLC22A3) and Its Missense Variants. submitted.
236. 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. PMC2771176
235. 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. PMC2790034
234. Gruswitz F, Chaudhary S, Ho J, Schlessinger A, Bobak P, Ho C, Sali A, Westhoff C, Stroud R. Renal Ammonia Transport and the Structure of the Human Rhesus Glycoprotein RhCG at 2.1 A. submitted.
233. Barkan D, Hostetter D, Mahrus S, Pieper U, Wells J, Craik C, Sali A. Prediction of Protease Substrates using Sequence and Structural Features. submitted.
232. 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. PMC2814252
231. Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comp Biol 6, e1000668, 2010. PMC2816688
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. PMC2725293
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. PMC2780624
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. PMC2742445
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. PMCID TBD by Journal
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. PMC2680734
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 USA 29, 11943-11947, 2009. PMC2715492
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. PMC2687990
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. PMCID TBD by Journal
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. PMC2705707
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. PMC2682653
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. PMC2667270
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. PMC2739730
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. PMC2774249
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. PMC2774440
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. PMC2659619
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. PMC2756966
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. PMC2686492
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. PMC2693957
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. PMCID TBD by Journal
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 USA 105, 9610-9615, 2008. PMC2474495
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. PMC2566540
208. Chiang RA, Sali A, Babbitt PC. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 4, e1000142, 2008. PMC2453236
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. PMC2279195
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. PMC2745287
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. PMC2578807
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. PMC2600884
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. PMC2587343
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. PMCID TBD by Journal
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. PMC2430716
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. PMC2409374
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. PMC2775484
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.
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.
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 Bioinformatics Chapter 5, Unit 5.6.1-5.6.30, 2006.
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. Current Protocols in 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 USA 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 USA 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, John Wiley & Sons, Totowa, NJ, 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., Totowa, NJ, 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., Oxford, UK, 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, Totowa, 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, Totowa, NJ, 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 USA 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, Oxford, UK, 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 USA 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 USA 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 USA 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 USA 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, LYNGBY, DENMARK, 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., LYNGBY, DENMARK, 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., Totowa, NJ, 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, London, 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, London, 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., LYNGBY, DENMARK, 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., London, 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, London, UK, 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, Berlin, West Germany; New York, New York, USA., 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.