Andrej Sali - Publications

Affiliations: 
1995-2002 Rockefeller University, New York, NY, United States 
 2003- Pharmacy University of California, San Francisco, San Francisco, CA 
Area:
protein structure, protein function, macromolecular assemblies, annotating protein function
Website:
https://pharmacy.ucsf.edu/andrej-sali

395 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Echeverria I, Braberg H, Krogan NJ, Sali A. Structure snapshot: Integrative structure determination of histones H3 and H4 using genetic interactions. The Febs Journal. PMID 35298864 DOI: 10.1111/febs.16435  0.62
2022 Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. Integration of software tools for integrative modeling of biomolecular systems. Journal of Structural Biology. 107841. PMID 35149213 DOI: 10.1016/j.jsb.2022.107841  0.526
2022 Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. From systems to structure - using genetic data to model protein structures. Nature Reviews. Genetics. PMID 35013567 DOI: 10.1038/s41576-021-00441-w  0.689
2021 Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, ... ... Sali A, et al. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. PMID 34982960 DOI: 10.1016/j.cell.2021.12.015  0.658
2021 Vallat B, Webb B, Fayazi M, Voinea S, Tangmunarunkit H, Ganesan SJ, Lawson CL, Westbrook JD, Kesselman C, Sali A, Berman HM. New system for archiving integrative structures. Acta Crystallographica. Section D, Structural Biology. 77: 1486-1496. PMID 34866606 DOI: 10.1107/S2059798321010871  0.724
2021 Huang F, Nguyen TT, Echeverria I, Ramachandran R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. Elife. 10. PMID 34821217 DOI: 10.7554/eLife.68473  0.633
2021 Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Goodsell DS, Ghosh S, Kramer Green R, ... ... Sali A, et al. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein Science : a Publication of the Protein Society. PMID 34676613 DOI: 10.1002/pro.4213  0.738
2021 Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharath K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A. Bayesian metamodeling of complex biological systems across varying representations. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34453000 DOI: 10.1073/pnas.2104559118  0.332
2021 Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. IMProv: A Resource for Crosslink-Driven Structure Modeling that Accommodates Protein Dynamics. Molecular & Cellular Proteomics : McP. 100139. PMID 34418567 DOI: 10.1016/j.mcpro.2021.100139  0.405
2021 Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Characterization of a A3G-Vif-CRL5-CBFβ structure using a cross-linking mass spectrometry pipeline for integrative modeling of host-pathogen complexes. Molecular & Cellular Proteomics : McP. 100132. PMID 34389466 DOI: 10.1016/j.mcpro.2021.100132  0.831
2021 Sali A. From integrative structural biology to cell biology. The Journal of Biological Chemistry. 100743. PMID 33957123 DOI: 10.1016/j.jbc.2021.100743  0.44
2021 Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA. CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife. 10. PMID 33949948 DOI: 10.7554/eLife.65168  0.627
2021 Yu Y, Li S, Ser Z, Sanyal T, Choi K, Wan B, Kuang H, Sali A, Kentsis A, Patel DJ, Zhao X. Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33941673 DOI: 10.1073/pnas.2026844118  0.357
2021 Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, ... ... Sali A, et al. Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2. Biorxiv : the Preprint Server For Biology. PMID 33851164 DOI: 10.1101/2021.04.08.438911  0.308
2021 Salcedo EC, Winter MB, Khuri N, Knudsen GM, Sali A, Craik CS. Global Protease Activity Profiling Identifies HER2-Driven Proteolysis in Breast Cancer. Acs Chemical Biology. PMID 33765766 DOI: 10.1021/acschembio.0c01000  0.476
2021 Tran TH, Nguyen JV, Stecula A, Akutagawa J, Moorman AV, Braun BS, Sali A, Mullighan CG, Shah NP, Dai Y, Devidas M, Roberts KG, Smith CC, Loh ML. The T681I mutation is highly resistant to imatinib and dasatinib and detectable in clinical samples prior to treatment. Haematologica. PMID 33626861 DOI: 10.3324/haematol.2020.261354  0.277
2021 Webb B, Sali A. Protein Structure Modeling with MODELLER. Methods in Molecular Biology (Clifton, N.J.). 2199: 239-255. PMID 33125654 DOI: 10.1007/978-1-0716-0892-0_14  0.441
2020 Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure (London, England : 1993). PMID 33412091 DOI: 10.1016/j.str.2020.12.006  0.262
2020 Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, ... ... Sali A, et al. Genetic interaction mapping informs integrative structure determination of protein complexes. Science (New York, N.Y.). 370. PMID 33303586 DOI: 10.1126/science.aaz4910  0.759
2020 White KL, Singla J, Loconte V, Chen JH, Ekman A, Sun L, Zhang X, Francis JP, Li A, Lin W, Tseng K, McDermott G, Alber F, Sali A, Larabell C, et al. Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Science Advances. 6. PMID 33298443 DOI: 10.1126/sciadv.abc8262  0.254
2020 Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Christie CH, Dalenberg K, Di Costanzo L, Duarte JM, Dutta S, Feng Z, Ganesan S, Goodsell DS, Ghosh S, ... ... Sali A, et al. RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Research. PMID 33211854 DOI: 10.1093/nar/gkaa1038  0.739
2020 Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A. Using Integrative Modeling Platform to Compute, Validate, and Archive a Model of a Protein Complex Structure. Protein Science : a Publication of the Protein Society. PMID 33166013 DOI: 10.1002/pro.3995  0.736
2020 Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, ... ... Sali A, et al. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure (London, England : 1993). PMID 33065067 DOI: 10.1016/j.str.2020.09.011  0.337
2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, ... ... Sali A, et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.). PMID 33060197 DOI: 10.1126/science.abe9403  0.796
2020 Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. The Journal of Cell Biology. 219. PMID 32785687 DOI: 10.1083/Jcb.202006159  0.237
2020 Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. Structural basis of CD4 downregulation by HIV-1 Nef. Nature Structural & Molecular Biology. PMID 32719457 DOI: 10.1038/S41594-020-0463-Z  0.677
2020 Qiao Y, Wang Z, Tan F, Chen J, Lin J, Yang J, Li H, Wang X, Sali A, Zhang L, Zhong G. Enhancer Reprogramming within Pre-existing Topologically Associated Domains Promotes TGF-β-Induced EMT and Cancer Metastasis. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 32526202 DOI: 10.1016/J.Ymthe.2020.05.026  0.238
2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, ... ... Sali A, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. Biorxiv : the Preprint Server For Biology. PMID 32511329 DOI: 10.1101/2020.03.22.002386  0.788
2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, ... ... Sali A, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/S41586-020-2286-9  0.789
2020 Ganesan SJ, Feyder MJ, Chemmama IE, Fang F, Rout MP, Chait BT, Shi Y, Munson M, Sali A. Integrative Structure and Function of the Yeast Exocyst Complex. Protein Science : a Publication of the Protein Society. PMID 32239688 DOI: 10.1002/Pro.3863  0.399
2020 Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L. Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling. Proceedings of the National Academy of Sciences of the United States of America. PMID 32034103 DOI: 10.1073/Pnas.1915542117  0.728
2019 Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, ... ... Sali A, et al. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993). PMID 31780431 DOI: 10.1016/J.Str.2019.11.002  0.821
2019 Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A. SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. Progress in Biophysics and Molecular Biology. PMID 31570166 DOI: 10.1016/J.Pbiomolbio.2019.09.003  0.546
2019 Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. Modeling Biological Complexes Using Integrative Modeling Platform. Methods in Molecular Biology (Clifton, N.J.). 2022: 353-377. PMID 31396911 DOI: 10.1007/978-1-4939-9608-7_15  0.733
2019 Vallat B, Webb B, Westbrook J, Sali A, Berman HM. Archiving and disseminating integrative structure models. Journal of Biomolecular Nmr. PMID 31278630 DOI: 10.1007/S10858-019-00264-2  0.595
2019 Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell. 177: 1384-1403. PMID 31150619 DOI: 10.1016/J.Cell.2019.05.016  0.406
2019 Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. Glutamine side chain 13C=18O as a non-perturbative IR probe of amyloid fibril hydration and assembly. Journal of the American Chemical Society. PMID 30998340 DOI: 10.1021/Jacs.9B00577  0.288
2019 Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. Elife. 8. PMID 30855230 DOI: 10.7554/Elife.43630  0.648
2019 Viswanath S, Sali A. Optimizing model representation for integrative structure determination of macromolecular assemblies. Proceedings of the National Academy of Sciences of the United States of America. 116: 540-545. PMID 30587581 DOI: 10.1073/Pnas.1814649116  0.374
2019 Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Author response: Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone Elife. DOI: 10.7554/Elife.43630.030  0.266
2019 Echeverria I, Braberg H, Cimermancic P, Pellarin R, Schneidman D, Shiver A, Gross C, Krogan N, Sali A. Modeling of Protein Complex Architectures using Combinatorial Genetic Perturbations Biophysical Journal. 116: 419a-420a. DOI: 10.1016/J.Bpj.2018.11.2261  0.62
2019 Berman H, Vallat B, Westbrook J, Webb B, Sali A. Archiving of Integrative/Hybrid Structural Models Biophysical Journal. 116: 329a. DOI: 10.1016/J.Bpj.2018.11.1785  0.41
2018 Schneidman-Duhovny D, Khuri N, Dong GQ, Winter MB, Shifrut E, Friedman N, Craik CS, Pratt KP, Paz P, Aswad F, Sali A. Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. Plos One. 13: e0206654. PMID 30399156 DOI: 10.1371/Journal.Pone.0206654  0.502
2018 Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R. Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling. Structure (London, England : 1993). PMID 30393052 DOI: 10.1016/J.Str.2018.09.011  0.58
2018 Jishage M, Yu X, Shi Y, Ganesan SJ, Chen WY, Sali A, Chait BT, Asturias FJ, Roeder RG. Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nature Structural & Molecular Biology. 25: 859-867. PMID 30190596 DOI: 10.1038/S41594-018-0118-5  0.24
2018 Gaber A, Kim SJ, Kaake RM, Benčina M, Krogan N, Šali A, Pavšič M, Lenarčič B. EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Scientific Reports. 8: 13269. PMID 30185875 DOI: 10.1038/S41598-018-31482-7  0.645
2018 Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods in Enzymology. 606: 1-71. PMID 30097089 DOI: 10.1016/Bs.Mie.2018.06.004  0.363
2018 Yoshizawa T, Ali R, Jiou J, Fung HYJ, Burke KA, Kim SJ, Lin Y, Peeples WB, Saltzberg D, Soniat M, Baumhardt JM, Oldenbourg R, Sali A, Fawzi NL, Rosen MK, et al. Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites. Cell. 173: 693-705.e22. PMID 29677513 DOI: 10.1016/J.Cell.2018.03.003  0.689
2018 Vallat B, Webb B, Westbrook JD, Sali A, Berman HM. Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. Structure (London, England : 1993). PMID 29657133 DOI: 10.1016/J.Str.2018.03.011  0.572
2018 Singla J, McClary KM, White KL, Alber F, Sali A, Stevens RC. Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell. Cell. 173: 11-19. PMID 29570991 DOI: 10.1016/J.Cell.2018.03.014  0.367
2018 Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, ... ... Sali A, et al. Integrative structure and functional anatomy of a nuclear pore complex. Nature. 555: 475-482. PMID 29539637 DOI: 10.1017/S1431927618006542  0.801
2018 Guy AJ, Irani V, Beeson JG, Webb B, Sali A, Richards JS, Ramsland PA. Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. Scientific Reports. 8: 4355. PMID 29531293 DOI: 10.1038/S41598-018-22592-3  0.353
2018 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, ... ... Sali A, et al. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 7. PMID 29377793 DOI: 10.7554/Elife.31097  0.666
2018 Echeverria I, Sali A. Integrative Structure Determination of Protein Complexes by Inferred Structural Equivalence Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.383  0.649
2018 Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor K, Yabut KC, Umbreit NT, Meehl J, Jones MH, Velazquez-Muriel J, Winey M, Rayment I, Davis TN, Sali A, Muller ED. A Bayesian Integrative Structure Model of the Yeast Centrosome Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.240  0.266
2018 Joong Kim S, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Upla P, Chemmama IE, Pellarin R, Echeverria I, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. Structure and Functional Anatomy of the Nuclear Pore Complex Biophysical Journal. 114: 372a. DOI: 10.1016/J.Bpj.2017.11.2063  0.776
2018 Vallat B, Webb B, Westbrook J, Sali A, Berman H. A Data Dictionary and Prototype Deposition System for Archiving Integrative/Hybrid Models Biophysical Journal. 114: 342a. DOI: 10.1016/J.Bpj.2017.11.1909  0.41
2017 Viswanath S, Chemmama IE, Cimermancic P, Sali A. Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures. Biophysical Journal. 113: 2344-2353. PMID 29211988 DOI: 10.1016/J.Bpj.2017.10.005  0.351
2017 Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik CS. Immunoproteasome functions explained by divergence in cleavage specificity and regulation. Elife. 6. PMID 29182146 DOI: 10.7554/Elife.27364  0.482
2017 Webb B, Sali A. Protein Structure Modeling with MODELLER. Methods in Molecular Biology (Clifton, N.J.). 1654: 39-54. PMID 28986782 DOI: 10.1007/978-1-4939-7231-9_4  0.441
2017 Jahangiri A, Nguyen A, Chandra A, Sidorov MK, Yagnik G, Rick J, Han SW, Chen W, Flanigan PM, Schneidman-Duhovny D, Mascharak S, De Lay M, Imber B, Park CC, Matsumoto K, ... ... Sali A, et al. Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973887 DOI: 10.1073/Pnas.1701821114  0.265
2017 Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with IMP. Protein Science : a Publication of the Protein Society. PMID 28960548 DOI: 10.1002/Pro.3311  0.42
2017 Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure (London, England : 1993). 25: 1317-1318. PMID 28877501 DOI: 10.1016/J.Str.2017.08.001  0.692
2017 Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, et al. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallographica. Section D, Structural Biology. 73: 710-728. PMID 28876235 DOI: 10.1107/S2059798317011597  0.572
2017 Wang X, Chemmama IE, Yu C, Huszagh A, Xu Y, Viner R, Block SA, Cimermancic P, Rychnovsky SD, Ye Y, Sali A, Huang L. The Proteasome-Interacting Ecm29 Protein Disassembles the 26S Proteasome in Response to Oxidative Stress. The Journal of Biological Chemistry. PMID 28821611 DOI: 10.1074/Jbc.M117.803619  0.313
2017 Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, ... Sali A, et al. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Molecular Biology of the Cell. PMID 28814505 DOI: 10.1091/Mbc.E17-06-0397  0.806
2017 Stecula A, Schlessinger A, Giacomini KM, Sali A. Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer. Biochemistry. PMID 28661652 DOI: 10.1021/Acs.Biochem.7B00339  0.346
2017 Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Reports. 19: 2033-2044. PMID 28591576 DOI: 10.1016/J.Celrep.2017.05.029  0.682
2017 Khuri N, Zur AA, Wittwer MB, Lin L, Yee SW, Sali A, Giacomini KM. Computational Discovery And Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1. Journal of Chemical Information and Modeling. PMID 28562037 DOI: 10.1021/Acs.Jcim.6B00720  0.305
2017 Chen Q, Vieth M, Timm DE, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Zeng W, Lu J, Liu L. Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages. Plos One. 12: e0175758. PMID 28406969 DOI: 10.1371/Journal.Pone.0175758  0.347
2017 Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg CH, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, ... ... Sali A, et al. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Molecular & Cellular Proteomics : McP. PMID 28292943 DOI: 10.1074/Mcp.M116.065326  0.384
2017 Manna PT, Obado SO, Boehm C, Gadelha C, Sali A, Chait BT, Rout MP, Field MC. Lineage-specific proteins essential for endocytosis in trypanosomes. Journal of Cell Science. PMID 28232524 DOI: 10.1242/Jcs.191478  0.308
2017 Chen EC, Khuri N, Liang X, Stecula A, Chien HC, Yee SW, Huang Y, Sali A, Giacomini KM. Discovery of Competitive and Non-competitive Ligands of the Organic Cation Transporter 1 (OCT1; SLC22A1). Journal of Medicinal Chemistry. PMID 28230985 DOI: 10.1021/Acs.Jmedchem.6B01317  0.285
2017 Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure (London, England : 1993). PMID 28162953 DOI: 10.1016/J.Str.2017.01.006  0.784
2017 Winter MB, Greca FL, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik CS. Author response: Immunoproteasome functions explained by divergence in cleavage specificity and regulation Elife. DOI: 10.7554/Elife.27364.030  0.482
2017 Vallat B, Webb B, Westbrook J, Sali A, Berman H. A data dictionary for archiving integrative/hybrid models Acta Crystallographica Section a Foundations and Advances. 73: C542-C542. DOI: 10.1107/S2053273317090313  0.41
2017 Vallat B, Webb B, Westbrook J, Sali A, Berman H. Small-angle scattering data representation in SASCIF and integrative/hybrid methods dictionary Acta Crystallographica Section a Foundations and Advances. 73: C1441-C1441. DOI: 10.1107/S2053273317081359  0.41
2017 Chemmama IE, Greenberg CH, Sali A. Multi-State Modeling of Biomolecules by Satisfaction of Spatial Restraints from Single-Particle Electron Microscopy Images Biophysical Journal. 112: 3-6. DOI: 10.1016/J.Bpj.2016.11.1875  0.338
2017 Raveh B, Karp J, Sparks S, Timney B, Cowburn D, Rout MP, Sali A. Striking the Balance between Selectivity and Efficiency: An Integrative Model of Nucleocytoplasmic Transport Biophysical Journal. 112: 239a. DOI: 10.1016/J.Bpj.2016.11.1308  0.492
2016 Fromme P, Sali A. Editorial overview: Biophysical and molecular biological methods. Current Opinion in Structural Biology. PMID 27908508 DOI: 10.1016/J.Sbi.2016.11.015  0.266
2016 Barkan DT, Cheng XL, Celino H, Tran TT, Bhandari A, Craik CS, Sali A, Smythe ML. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. Bmc Bioinformatics. 17: 481. PMID 27881076 DOI: 10.1186/S12859-016-1350-9  0.499
2016 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, et al. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell. PMID 27839866 DOI: 10.1016/J.Cell.2016.10.028  0.68
2016 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. The Journal of Physical Chemistry. B. PMID 27807976 DOI: 10.1021/Acs.Jpcb.6B09358  0.361
2016 Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Protein Science. 86: 2.9.1-2.9.37. PMID 27801516 DOI: 10.1002/cpps.20  0.437
2016 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. PMID 27731797 DOI: 10.7554/Elife.15910  0.717
2016 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. The Journal of Cell Biology. PMID 27697925 DOI: 10.1083/Jcb.201601004  0.661
2016 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. Journal of Virology. PMID 27440899 DOI: 10.1128/Jvi.01106-16  0.414
2016 Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Bioinformatics. 54: 5.6.1-5.6.37. PMID 27322406 DOI: 10.1002/cpbi.3  0.437
2016 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. Molecular & Cellular Proteomics : McP. PMID 27250206 DOI: 10.1074/Mcp.M115.056473  0.35
2016 Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Research. PMID 27151198 DOI: 10.1093/Nar/Gkw389  0.394
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.808
2016 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 27091992 DOI: 10.1073/Pnas.1522663113  0.548
2016 Sprowl JA, Ong SS, Gibson AA, Hu S, Du G, Lin W, Li L, Bharill S, Ness RA, Stecula A, Offer SM, Diasio RB, Nies AT, Schwab M, Cavaletti G, ... ... Sali A, et al. A phosphotyrosine switch regulates organic cation transporters. Nature Communications. 7: 10880. PMID 26979622 DOI: 10.1038/Ncomms10880  0.27
2016 Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. Journal of Structural Biology. PMID 26968363 DOI: 10.1016/J.Jsb.2016.03.006  0.417
2016 Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. Journal of Molecular Biology. PMID 26854760 DOI: 10.1016/J.Jmb.2016.01.029  0.814
2016 Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. Author response: Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex Elife. DOI: 10.7554/Elife.15910.025  0.708
2016 Jahangiri A, Sidorov M, Han SW, Chen W, Rick J, Schneidman-Duhovny D, Mascharak S, Lay MD, Wagner J, Castro B, Imber B, Flanigan P, Kuang R, Lu K, Bergers G, ... Sali A, et al. DRES-11. A CROSS-ACTIVATING c-Met/β1 INTEGRIN COMPLEX DRIVES THERAPEUTIC RESISTANCE IN GLIOBLASTOMA Neuro-Oncology. 18. DOI: 10.1093/Neuonc/Now212.221  0.266
2016 Kim SJ, Fernandez-Martinez J, Shi Y, Upla P, Pellarin R, Chemmama IE, Nudelman I, Stokes DL, Chait BT, Sali A, Rout MP. Molecular Architecture of the Nup82 Complex, the Cytoplasmic mRNA Export Platform in the Nuclear Pore Complex Biophysical Journal. 110: 347a. DOI: 10.1016/J.Bpj.2015.11.1869  0.661
2015 Lasater EA, Massi ES, Stecula A, Politi J, Tan SK, Smith CC, Gunthorpe M, Holmes JP, Chehab F, Sali A, Shah NP. Novel TKI-resistant BCR-ABL1 gatekeeper residue mutations retain in vitro sensitivity to axitinib. Leukemia. PMID 26511402 DOI: 10.1038/Leu.2015.303  0.57
2015 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. The Journal of Biological Chemistry. PMID 26475863 DOI: 10.1074/Jbc.M115.689604  0.744
2015 Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. Journal of Medicinal Chemistry. 58: 8285-91. PMID 26443011 DOI: 10.1021/Acs.Jmedchem.5B01216  0.799
2015 Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. A strategy for dissecting the architectures of native macromolecular assemblies. Nature Methods. PMID 26436480 DOI: 10.1038/Nmeth.3617  0.354
2015 Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. Elife. 4. PMID 26402457 DOI: 10.7554/Elife.08719  0.579
2015 Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Molecular Cell. 59: 794-806. PMID 26340423 DOI: 10.1016/J.Molcel.2015.07.016  0.323
2015 Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. Plos Computational Biology. 11: e1004362. PMID 26312481 DOI: 10.1371/Journal.Pcbi.1004362  0.407
2015 Roy Choudhury A, Sikorska E, van den Boom J, Bayer P, Popenda Ł, 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. PMID 26291722 DOI: 10.1371/Journal.Pone.0135455  0.362
2015 Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophysical Journal. 109: 793-805. PMID 26287631 DOI: 10.1016/J.Bpj.2015.06.065  0.692
2015 Smith CC, Lin K, Stecula A, Sali A, Shah NP. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia. PMID 26108694 DOI: 10.1038/Leu.2015.165  0.588
2015 Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (London, England : 1993). PMID 26095030 DOI: 10.1016/J.Str.2015.05.013  0.808
2015 Lima CD, Sali A, Kostic M. Growing an editorial board for an ever expanding field. Structure (London, England : 1993). 23: 605. PMID 25862929 DOI: 10.1016/J.Str.2015.03.004  0.384
2015 Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 49: 8.19.1-8.19.16. PMID 25754993 DOI: 10.1002/0471250953.Bi0819S49  0.3
2015 Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nature Structural & Molecular Biology. 22: 132-7. PMID 25599398 DOI: 10.1038/Nsmb.2953  0.256
2015 Politis A, Schmidt C, Tjioe E, Sandercock AM, Lasker K, Gordiyenko Y, Russel D, Sali A, Robinson CV. Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex. Chemistry & Biology. 22: 117-28. PMID 25544043 DOI: 10.1016/J.Chembiol.2014.11.010  0.344
2015 Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Author response: Molecular architecture of the yeast Mediator complex Elife. DOI: 10.7554/Elife.08719.022  0.505
2015 Shi Y, Fridy PC, Thompson MK, Rout MP, Wang QJ, Fernandez-Martinez J, Chait BT, Li Y, Sali A, Pellarin R. Modeling exosome complexes from cross-link MS data Nature Methods. 12. DOI: 10.5281/Zenodo.60731  0.266
2015 Choudhury AR, Sikorska E, Van Den Boom J, Bayer P, Popenda Ł, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novic M. Structural model of the bilitranslocase transmembrane domain supported by NMR and FRET data Plos One. 10. DOI: 10.1371/journal.pone.0135455  0.266
2015 Reid R, Sgobba M, Raveh B, Rastelli G, Sali A, Santi DV. Analytical and Simulation-Based Models for Drug Release and Gel-Degradation in a Tetra-PEG Hydrogel Drug-Delivery System Macromolecules. 48: 7359-7369. DOI: 10.1021/Acs.Macromol.5B01598  0.243
2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex. Cell. 159: 1227-1228. PMID 28898626 DOI: 10.1016/J.Cell.2014.11.001  0.266
2014 Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA. A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. Plos Computational Biology. 10: e1004016. PMID 25474254 DOI: 10.1371/Journal.Pcbi.1004016  0.277
2014 Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Bioinformatics. 47: 5.6.1-32. PMID 25199792 DOI: 10.1002/0471250953.bi0506s47  0.456
2014 Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in integrative structural modeling. Current Opinion in Structural Biology. 28: 96-104. PMID 25173450 DOI: 10.1016/J.Sbi.2014.08.001  0.333
2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40Sâ‹…eIF1â‹…eIF3 translation initiation complex. Cell. 158: 1123-35. PMID 25171412 DOI: 10.1016/J.Cell.2014.07.044  0.339
2014 Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Molecular & Cellular Proteomics : McP. 13: 2927-43. PMID 25161197 DOI: 10.1074/Mcp.M114.041673  0.73
2014 Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. Journal of Molecular Biology. 426: 3713-28. PMID 25149264 DOI: 10.1016/J.Jmb.2014.07.033  0.317
2014 Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, ... Sali A, et al. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Molecular & Cellular Proteomics : McP. 13: 2911-26. PMID 25139911 DOI: 10.1074/Mcp.M114.040915  0.799
2014 Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data. Molecular & Cellular Proteomics : McP. 13: 2812-23. PMID 25139910 DOI: 10.1074/Mcp.M114.040824  0.824
2014 Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Structure (London, England : 1993). 22: 1239-51. PMID 25087511 DOI: 10.1016/J.Str.2014.04.019  0.304
2014 Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S. Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway. Molecular & Cellular Proteomics : McP. 13: 2855-70. PMID 25073740 DOI: 10.1074/Mcp.M114.039388  0.688
2014 Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 158: 412-21. PMID 25036635 DOI: 10.1016/J.Cell.2014.06.034  0.414
2014 Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. Journal of Chemical Information and Modeling. 54: 1687-99. PMID 24802635 DOI: 10.1021/Ci5001554  0.588
2014 Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. Journal of Molecular Biology. 426: 2393-404. PMID 24726919 DOI: 10.1016/J.Jmb.2014.04.001  0.319
2014 Webb B, Sali A. Protein structure modeling with MODELLER. Methods in Molecular Biology (Clifton, N.J.). 1137: 1-15. PMID 24573470 DOI: 10.1007/978-1-4939-0366-5_1  0.441
2014 Spill YG, 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. Journal of Synchrotron Radiation. 21: 203-8. PMID 24365937 DOI: 10.1107/S1600577513030117  0.687
2014 Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 42: D336-46. PMID 24271400 DOI: 10.1093/Nar/Gkt1144  0.833
2014 Webb B, Lasker K, Velázquez-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. Methods in Molecular Biology (Clifton, N.J.). 1091: 277-95. PMID 24203340 DOI: 10.1007/978-1-62703-691-7_20  0.423
2014 Molnar KS, Goldberg SD, Sali A, Goulian M, Bonomi M, DeGrado WF, Clinthorne GD, Gonzalez G, Pellarin R. Multi-state modeling of the PhoQ two-component system Structure. 22: 1239-1251. DOI: 10.5281/Zenodo.46600  0.266
2014 Zeng-Elmore X, Tang Y, Gao X, Schneidman-Duhovny D, Cote RH, Zhang X, Chalkley RJ, Chu F, Kozacka KA, Sali A, Pellarin R. Modeling of the phosphodiesterase (PDE6) Journal of Molecular Biology. 426: 3713-3728. DOI: 10.5281/Zenodo.46599  0.266
2014 Politis A, Gordiyenko Y, Lasker K, Russel D, Sandercock AM, Robinson CV, Schmidt C, Tjioe E, Sali A. Mass Spec Benchmark Chemistry & Biology. 22: 117-128. DOI: 10.5281/Zenodo.46595  0.266
2014 Bonomi M, Sundin BA, Jaschob D, Davis TN, Russel D, Riffle M, Kim SJ, Muller EGD, Sali A, Pellarin R, Ramsden R. Benchmark of the FRETR Bayesian restraint Molecular & Cellular Proteomics. 13: 2812-2823. DOI: 10.5281/Zenodo.46558  0.266
2014 Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Rout M, Sali A, Chait B. Modeling of the Nup84 subcomplex of the Nuclear Pore Complex Molecular & Cellular Proteomics. 13. DOI: 10.5281/Zenodo.46266  0.266
2014 Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA. Qualitative model for the evolution of NRPS/PKS domains. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1004016.G004  0.266
2013 Ryan CJ, Cimerman?i? P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. High-resolution network biology: connecting sequence with function. Nature Reviews. Genetics. 14: 865-79. PMID 24197012 DOI: 10.1038/Nrg3574  0.379
2013 Martínez-Jiménez 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 Computational Biology. 9: e1003253. PMID 24098102 DOI: 10.1371/Journal.Pcbi.1003253  0.593
2013 Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. Journal of the American Chemical Society. 135: 16595-609. PMID 24093873 DOI: 10.1021/Ja4083717  0.328
2013 Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics (Oxford, England). 29: 3158-66. PMID 24078704 DOI: 10.1093/Bioinformatics/Btt560  0.35
2013 Lima CD, Sali A, Kostic M. Celebrating 20 years of Structure. Structure (London, England : 1993). 21: 1477-8. PMID 24010704 DOI: 10.1016/J.Str.2013.08.015  0.426
2013 Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophysical Journal. 105: 962-74. PMID 23972848 DOI: 10.1016/J.Bpj.2013.07.020  0.41
2013 Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 52: 6525-36. PMID 23972005 DOI: 10.1021/Bi400750A  0.527
2013 Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. Structure-guided discovery of new deaminase enzymes. Journal of the American Chemical Society. 135: 13927-33. PMID 23968233 DOI: 10.1021/Ja4066078  0.563
2013 Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. Consequences of domain insertion on sequence-structure divergence in a superfold. Proceedings of the National Academy of Sciences of the United States of America. 110: E3381-7. PMID 23959887 DOI: 10.1073/Pnas.1305519110  0.336
2013 Weinkam P, Sali A. Mapping polymerization and allostery of hemoglobin S using point mutations. The Journal of Physical Chemistry. B. 117: 13058-68. PMID 23957820 DOI: 10.1021/Jp4025156  0.304
2013 Schlessinger A, Yee SW, Sali A, Giacomini KM. SLC classification: An update Clinical Pharmacology and Therapeutics. 94: 19-23. PMID 23778706 DOI: 10.1038/Clpt.2013.73  0.361
2013 Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure (London, England : 1993). 21: 875-81. PMID 23747111 DOI: 10.1016/J.Str.2013.04.020  0.79
2013 Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM. Structural basis for alternating access of a eukaryotic calcium/proton exchanger Nature. 499: 107-110. PMID 23685453 DOI: 10.1038/Nature12233  0.455
2013 Gradišar H, Božič S, Doles T, Vengust D, Hafner-Bratkovič I, Mertelj A, Webb B, Šali A, Klavžar S, Jerala R. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nature Chemical Biology. 9: 362-6. PMID 23624438 DOI: 10.1038/Nchembio.1248  0.324
2013 Schlessinger A, Khuri N, Giacomini KM, Sali A. Molecular modeling and ligand docking for solute carrier (SLC) transporters. Current Topics in Medicinal Chemistry. 13: 843-56. PMID 23578028 DOI: 10.2174/1568026611313070007  0.356
2013 van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA. Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proceedings of the National Academy of Sciences of the United States of America. 110: 6943-8. PMID 23569277 DOI: 10.1073/Pnas.1221011110  0.293
2013 Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM. Crystal structure of a eukaryotic phosphate transporter. Nature. 496: 533-6. PMID 23542591 DOI: 10.1038/Nature12042  0.497
2013 Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proceedings of the National Academy of Sciences of the United States of America. 110: 5480-5. PMID 23509259 DOI: 10.1073/Pnas.1218165110  0.264
2013 Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, ... ... Sali A, et al. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure (London, England : 1993). 21: 560-71. PMID 23499021 DOI: 10.1016/J.Str.2013.02.005  0.787
2013 Guttman M, Weinkam P, Sali A, Lee KK. All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins. Structure (London, England : 1993). 21: 321-31. PMID 23473666 DOI: 10.1016/J.Str.2013.02.004  0.38
2013 Ward AB, Sali A, Wilson IA. Biochemistry. Integrative structural biology. Science (New York, N.Y.). 339: 913-5. PMID 23430643 DOI: 10.1126/Science.1228565  0.466
2013 Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, ... ... Sali A, et al. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nature Structural & Molecular Biology. 20: 135-8. PMID 23381628 DOI: 10.1038/Nsmb.2508  0.668
2013 Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. Journal of the American Chemical Society. 135: 795-803. PMID 23256477 DOI: 10.1021/Ja309680B  0.534
2013 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. Journal of Medicinal Chemistry. 56: 781-95. PMID 23241029 DOI: 10.1021/Jm301302S  0.276
2013 Weinkam P, Chen YC, Pons J, Sali A. Impact of mutations on the allosteric conformational equilibrium. Journal of Molecular Biology. 425: 647-61. PMID 23228330 DOI: 10.1016/J.Jmb.2012.11.041  0.357
2013 Spill YG, Nilges M, Schneidman-Duhovny D, Webb B, Russel D, Kim SJ, Sali A. Benchmark of the SAXS Merge method Journal of Synchrotron Radiation. 203-208. DOI: 10.5281/Zenodo.46479  0.266
2012 Kolb P, Phan K, Gao ZG, Marko AC, Sali A, Jacobson KA. Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists. Plos One. 7: e49910. PMID 23185482 DOI: 10.1371/Journal.Pone.0049910  0.333
2012 Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proceedings of the National Academy of Sciences of the United States of America. 109: 18821-6. PMID 23112201 DOI: 10.1073/Pnas.1216549109  0.375
2012 Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, ... ... Sali A, et al. A method for integrative structure determination of protein-protein complexes. Bioinformatics (Oxford, England). 28: 3282-9. PMID 23093611 DOI: 10.1093/Bioinformatics/Bts628  0.743
2012 Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S. Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Biomacromolecules. 13: 3494-502. PMID 22974364 DOI: 10.1021/Bm300942C  0.683
2012 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 MW, Case D, Chazin WJ, ... ... Sali A, et al. In support of the BMRB. Nature Structural & Molecular Biology. 19: 854-60. PMID 22955930 DOI: 10.1038/Nsmb.2371  0.772
2012 Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A. High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. The Journal of Biological Chemistry. 287: 37745-56. PMID 22932902 DOI: 10.1074/Jbc.M112.388157  0.32
2012 Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. Strategic protein target analysis for developing drugs to stop dental caries. Advances in Dental Research. 24: 86-93. PMID 22899687 DOI: 10.1177/0022034512449837  0.378
2012 Schneidman-Duhovny D, Kim SJ, Sali A. Integrative structural modeling with small angle X-ray scattering profiles. Bmc Structural Biology. 12: 17. PMID 22800408 DOI: 10.1186/1472-6807-12-17  0.752
2012 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. Biological Chemistry. 393: 177-86. PMID 22718633 DOI: 10.1515/Hsz-2011-0219  0.299
2012 Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Molecular & Cellular Proteomics : McP. 11: 215-29. PMID 22645316 DOI: 10.1074/Mcp.O112.018366  0.314
2012 Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS. SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinformatics (Oxford, England). 28: 2072-3. PMID 22618536 DOI: 10.1093/Bioinformatics/Bts302  0.419
2012 Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N, Chiu EJ, Blain KY, Esquivies L, Kwon JH, Balana B, Pieper U, Sali A, Slesinger PA, Kwiatkowski W, Riek R, et al. Facile backbone structure determination of human membrane proteins by NMR spectroscopy. Nature Methods. 9: 834-9. PMID 22609626 DOI: 10.1038/Nmeth.2033  0.397
2012 Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, ... ... Sali A, et al. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata. Proteins. 80: 2110-6. PMID 22544723 DOI: 10.1002/Prot.24102  0.795
2012 Weinkam P, Pons J, Sali A. Structure-based model of allostery predicts coupling between distant sites. Proceedings of the National Academy of Sciences of the United States of America. 109: 4875-80. PMID 22403063 DOI: 10.1073/Pnas.1116274109  0.359
2012 Fernandez-Martinez J, Phillips J, Sekedat MD, Diaz-Avalos R, Velazquez-Muriel J, Franke JD, Williams R, Stokes DL, Chait BT, Sali A, Rout MP. Structure-function mapping of a heptameric module in the nuclear pore complex. The Journal of Cell Biology. 196: 419-34. PMID 22331846 DOI: 10.1083/Jcb.201109008  0.392
2012 Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, et al. Outcome of the first electron microscopy validation task force meeting. Structure (London, England : 1993). 20: 205-14. PMID 22325770 DOI: 10.1016/J.Str.2011.12.014  0.789
2012 Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods in Molecular Biology (Clifton, N.J.). 857: 331-50. PMID 22323229 DOI: 10.1007/978-1-61779-588-6_15  0.402
2012 Lasker K, Förster 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 1380-7. PMID 22307589 DOI: 10.1073/Pnas.1120559109  0.336
2012 Russel D, Lasker K, Webb B, Velázquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. Plos Biology. 10: e1001244. PMID 22272186 DOI: 10.1371/Journal.Pbio.1001244  0.387
2012 Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, ... Sali A, et al. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature. 481: 371-5. PMID 22190037 DOI: 10.1038/Nature10693  0.5
2012 Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, ... ... Sali A, et al. Global landscape of HIV-human protein complexes. Nature. 481: 365-70. PMID 22190034 DOI: 10.1038/Nature10719  0.5
2012 Pathare GR, Nagy I, Bohn S, Unverdorben P, Hubert A, Körner R, Nickell S, Lasker K, Sali A, Tamura T, Nishioka T, Förster F, Baumeister W, Bracher A. The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together. Proceedings of the National Academy of Sciences of the United States of America. 109: 149-54. PMID 22187461 DOI: 10.1073/Pnas.1117648108  0.338
2012 Fan H, Irwin JJ, Sali A. Virtual ligand screening against comparative protein structure models. Methods in Molecular Biology (Clifton, N.J.). 819: 105-26. PMID 22183533 DOI: 10.1007/978-1-61779-465-0_8  0.385
2012 Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. Journal of Structural Biology. 179: 269-78. PMID 21963794 DOI: 10.1016/J.Jsb.2011.09.006  0.388
2012 Lasker K, Webb BM, Yang Z, Ferrin TE, Sali A, Velázquez-Muriel JA. Modeling of the bacterial molecular chaperone GroEL using 3D EM data and cnmultifit Methods of Molecular Biology. 857. DOI: 10.5281/Zenodo.46596  0.266
2012 Joong Kim S, Sampathkumar P, Fernandez-Martinez J, Phillips J, Schneidman D, Matsui T, Tsuruta H, Sauder M, Burley SK, Rout M, Sali A. Integrative Structure Determination of the Components of the Nuclear Pore Complex by X-Ray Crystallography, Small Angle X-Ray Scattering, Electron Microscopy, NMR, and Comparative Modeling Biophysical Journal. 102: 619a. DOI: 10.1016/J.Bpj.2011.11.3371  0.784
2011 Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. Statistical potential for modeling and ranking of protein-ligand interactions. Journal of Chemical Information and Modeling. 51: 3078-92. PMID 22014038 DOI: 10.1021/Ci200377U  0.374
2011 Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 50: 9950-62. PMID 21999478 DOI: 10.1021/Bi201312U  0.687
2011 Choi JH, Yee SW, Ramirez AH, Morrissey KM, Jang GH, Joski PJ, Mefford JA, Hesselson SE, Schlessinger A, Jenkins G, Castro RA, Johns SJ, Stryke D, Sali A, Ferrin TE, et al. A common 5'-UTR variant in MATE2-K is associated with poor response to metformin. Clinical Pharmacology and Therapeutics. 90: 674-84. PMID 21956618 DOI: 10.1038/Clpt.2011.165  0.27
2011 Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nature Chemical Biology. 7: 769-78. PMID 21926995 DOI: 10.1038/Nchembio.662  0.369
2011 Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A. Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proceedings of the National Academy of Sciences of the United States of America. 108: 15810-5. PMID 21885739 DOI: 10.1073/Pnas.1106030108  0.324
2011 Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A. Modeling of proteins and their assemblies with the integrative modeling platform. Methods in Molecular Biology (Clifton, N.J.). 781: 377-97. PMID 21877292 DOI: 10.1007/978-1-61779-276-2_19  0.732
2011 Goble AM, Fan H, Sali A, Raushel FM. Discovery of a cytokinin deaminase. Acs Chemical Biology. 6: 1036-40. PMID 21823622 DOI: 10.1021/Cb200198C  0.276
2011 Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Research. 39: W167-70. PMID 21715383 DOI: 10.1093/Nar/Gkr490  0.395
2011 Field MC, Sali A, Rout MP. Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. The Journal of Cell Biology. 193: 963-72. PMID 21670211 DOI: 10.1083/Jcb.201102042  0.332
2011 Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 10: M110.006478. PMID 21454883 DOI: 10.1074/Mcp.M110.006478  0.327
2011 Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, ... ... Sali A, et al. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Proteins. 79: 1672-7. PMID 21365675 DOI: 10.1002/Prot.22973  0.753
2011 Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. Journal of the American Chemical Society. 133: 2080-3. PMID 21275375 DOI: 10.1021/Ja110157U  0.495
2011 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: 1917-27. PMID 21247091 DOI: 10.1021/Bi101788N  0.478
2011 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, Sjölander K, Ferrin TE, ... ... Sali A, et al. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research. 39: D465-74. PMID 21097780 DOI: 10.1093/nar/gkq1091  0.609
2011 Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile Journal of Structural Biology. 173: 461-471. PMID 20920583 DOI: 10.1016/J.Jsb.2010.09.023  0.461
2011 Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Letter to the editor Protein Science. 20: 4-5. DOI: 10.1002/Pro.555  0.663
2010 Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenetics and Genomics. 20: 687-99. PMID 20859243 DOI: 10.1097/Fpc.0B013E32833Fe789  0.25
2010 Lasker K, Sali A, Wolfson HJ. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins. 78: 3205-11. PMID 20827723 DOI: 10.1002/Prot.22845  0.413
2010 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 Science : a Publication of the Protein Society. 19: 2110-21. PMID 20799350 DOI: 10.1002/Pro.491  0.677
2010 Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, ... ... Sali A, et al. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 78: 3056-62. PMID 20737437 DOI: 10.1002/Prot.22829  0.633
2010 Lasker K, Phillips JL, Russel D, Velázquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A. Integrative structure modeling of macromolecular assemblies from proteomics data. Molecular & Cellular Proteomics : McP. 9: 1689-702. PMID 20507923 DOI: 10.1074/Mcp.R110.000067  0.41
2010 Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A. Prediction of protease substrates using sequence and structure features. Bioinformatics (Oxford, England). 26: 1714-22. PMID 20505003 DOI: 10.1093/Bioinformatics/Btq267  0.796
2010 Förster F, Lasker K, Nickell S, Sali A, Baumeister W. Toward an integrated structural model of the 26S proteasome. Molecular & Cellular Proteomics : McP. 9: 1666-77. PMID 20467039 DOI: 10.1074/Mcp.R000002-Mcp201  0.349
2010 Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, Stroud RM. Function of human Rh based on structure of RhCG at 2.1 A. Proceedings of the National Academy of Sciences of the United States of America. 107: 9638-43. PMID 20457942 DOI: 10.1073/Pnas.1003587107  0.525
2010 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, et al. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Proteins. 78: 1992-8. PMID 20310066 DOI: 10.1002/Prot.22707  0.761
2010 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 Science : a Publication of the Protein Society. 19: 412-28. PMID 20052679 DOI: 10.1002/Pro.320  0.744
2010 Lasker K, Wolfson HJ, Sali A. Structural Determination of Macromolecular Machines Guided By Proteomics and Electron Microscopy Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.346  0.37
2010 Kim SJ, Phillips J, Martel A, Schneidman D, Sauder M, Rout MP, Tsuruta H, Sali A. Determination of the Pseudo-Atomic Structure of Nuclear Pore Complex (NPC) Components by Small Angle X-Ray Scattering (SAXS) and Computational Modeling Biophysical Journal. 98: 461a. DOI: 10.1016/J.Bpj.2009.12.2506  0.725
2009 Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. Comprehensive molecular structure of the eukaryotic ribosome. Structure (London, England : 1993). 17: 1591-604. PMID 20004163 DOI: 10.1016/J.Str.2009.09.015  0.749
2009 Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. Molecular docking screens using comparative models of proteins. Journal of Chemical Information and Modeling. 49: 2512-27. PMID 19845314 DOI: 10.1021/Ci9003706  0.394
2009 Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM. Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy. Pharmacogenomics. 10: 1569-76. PMID 19842929 DOI: 10.2217/Pgs.09.119  0.259
2009 Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A. A survey of integral alpha-helical membrane proteins. Journal of Structural and Functional Genomics. 10: 269-80. PMID 19760129 DOI: 10.1007/S10969-009-9069-8  0.738
2009 Förster 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. Biochemical and Biophysical Research Communications. 388: 228-33. PMID 19653995 DOI: 10.1016/J.Bbrc.2009.07.145  0.353
2009 Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. Alignment of multiple protein structures based on sequence and structure features Protein Engineering, Design and Selection. 22: 569-574. PMID 19587024 DOI: 10.1093/Protein/Gzp040  0.411
2009 Nickell S, Beck F, Scheres SH, Korinek A, Förster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko JM, Carazo JM, Mann M, Baumeister W. Insights into the molecular architecture of the 26S proteasome. Proceedings of the National Academy of Sciences of the United States of America. 106: 11943-7. PMID 19581588 DOI: 10.1073/Pnas.0905081106  0.314
2009 DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT. Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Molecular & Cellular Proteomics : McP. 8: 2119-30. PMID 19525551 DOI: 10.1074/Mcp.M900038-Mcp200  0.315
2009 Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Science : a Publication of the Protein Society. 18: 1306-15. PMID 19472362 DOI: 10.1002/Pro.143  0.389
2009 Ortí 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 Neglected Tropical Diseases. 3: e418. PMID 19381286 DOI: 10.1371/Journal.Pntd.0000418  0.275
2009 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. PMID 19357100 DOI: 10.1093/Bioinformatics/Btp238  0.389
2009 Ortí 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. Nature Biotechnology. 27: 320-1. PMID 19352362 DOI: 10.1038/Nbt0409-320  0.266
2009 Lasker K, Topf M, Sali A, Wolfson HJ. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. Journal of Molecular Biology. 388: 180-94. PMID 19233204 DOI: 10.1016/J.Jmb.2009.02.031  0.758
2009 Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, Sali A. The structural dynamics of macromolecular processes. Current Opinion in Cell Biology. 21: 97-108. PMID 19223165 DOI: 10.1016/J.Ceb.2009.01.022  0.29
2009 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, ... ... Sali A, et al. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Journal of Structural and Functional Genomics. 10: 107-25. PMID 19219566 DOI: 10.1007/S10969-008-9056-5  0.825
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014  0.808
2009 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. Journal of Structural and Functional Genomics. 10: 193-208. PMID 19148774 DOI: 10.1007/S10969-008-9058-3  0.718
2009 Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, Stroud RM. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. Journal of Molecular Biology. 385: 820-30. PMID 19061901 DOI: 10.1016/J.Jmb.2008.11.021  0.741
2009 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. Journal of Structural and Functional Genomics. 10: 9-16. PMID 19031011 DOI: 10.1007/S10969-008-9046-7  0.74
2009 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 Research. 37: D347-54. PMID 18948282 DOI: 10.1093/nar/gkn791  0.741
2009 Kim SJ, Webb B, Förster F, Sali A. The combination of Small-Angle X-ray Scattering fitting and protein structure modeling in Integrative Modeling Platform Biophysical Journal. 96: 654a. DOI: 10.1016/J.Bpj.2008.12.3453  0.323
2008 Karchin R, Agarwal M, Sali A, Couch F, Beattie MS. Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Cancer Informatics. 6: 203-16. PMID 19043619 DOI: 10.4137/Cin.S618  0.337
2008 Agüero 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, ... ... Sali A, et al. Genomic-scale prioritization of drug targets: the TDR Targets database. Nature Reviews. Drug Discovery. 7: 900-7. PMID 18927591 DOI: 10.1038/Nrd2684  0.72
2008 Eramian D, Eswar N, Shen MY, Sali A. How well can the accuracy of comparative protein structure models be predicted? Protein Science : a Publication of the Protein Society. 17: 1881-93. PMID 18832340 DOI: 10.1110/Ps.036061.108  0.399
2008 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: 866-76. PMID 18722006 DOI: 10.1016/J.Cell.2008.08.012  0.752
2008 Förster 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. Journal of Molecular Biology. 382: 1089-106. PMID 18694757 DOI: 10.1016/J.Jmb.2008.07.074  0.463
2008 Chiang RA, Sali A, Babbitt PC. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. Plos Computational Biology. 4: e1000142. PMID 18670595 DOI: 10.1371/Journal.Pcbi.1000142  0.3
2008 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. Proceedings of the National Academy of Sciences of the United States of America. 105: 9610-5. PMID 18621707 DOI: 10.1073/Pnas.0803189105  0.786
2008 Eswar N, Eramian D, Webb B, Shen MY, Sali A. Protein structure modeling with MODELLER. Methods in Molecular Biology (Clifton, N.J.). 426: 145-59. PMID 18542861 DOI: 10.1007/978-1-60327-058-8_8  0.439
2008 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. Nature Structural & Molecular Biology. 15: 746-53. PMID 18536725 DOI: 10.1038/Nsmb.1436  0.797
2008 Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. Bmc Bioinformatics. 9: 249. PMID 18505562 DOI: 10.1186/1471-2105-9-249  0.378
2008 Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA. Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure (London, England : 1993). 16: 755-65. PMID 18462680 DOI: 10.1016/J.Str.2008.01.021  0.323
2008 Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure (London, England : 1993). 16: 535-48. PMID 18400176 DOI: 10.1016/J.Str.2008.01.007  0.729
2008 Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annual Review of Biochemistry. 77: 443-77. PMID 18318657 DOI: 10.1146/Annurev.Biochem.77.060407.135530  0.761
2008 Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure (London, England : 1993). 16: 295-307. PMID 18275820 DOI: 10.1016/J.Str.2007.11.016  0.78
2008 Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, ... ... Sali A, et al. Protein production and purification. Nature Methods. 5: 135-46. PMID 18235434 DOI: 10.1038/Nmeth.F.202  0.684
2008 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. Journal of Molecular Biology. 375: 331-6. PMID 18022194 DOI: 10.1016/J.Jmb.2007.10.027  0.751
2007 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 Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 2.9. PMID 18429317 DOI: 10.1002/0471140864.Ps0209S50  0.457
2007 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, ... ... Sali A, et al. Structural genomics of protein phosphatases. Journal of Structural and Functional Genomics. 8: 121-40. PMID 18058037 DOI: 10.1007/S10969-007-9036-1  0.669
2007 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. PMID 18046406 DOI: 10.1038/Nature06405  0.36
2007 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: 683-94. PMID 18046405 DOI: 10.1038/Nature06404  0.415
2007 Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 51-63. PMID 17990484  0.688
2007 Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Host pathogen protein interactions predicted by comparative modeling. Protein Science : a Publication of the Protein Society. 16: 2585-96. PMID 17965183 DOI: 10.1110/Ps.073228407  0.321
2007 Melo F, Sali A. Fold assessment for comparative protein structure modeling Protein Science. 16: 2412-2426. PMID 17905832 DOI: 10.1110/Ps.072895107  0.382
2007 Feyfant E, Sali A, Fiser A. Modeling mutations in protein structures Protein Science. 16: 2030-2041. PMID 17766392 DOI: 10.1110/Ps.072855507  0.357
2007 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: S4. PMID 17570147 DOI: 10.1186/1471-2105-8-S4-S4  0.424
2007 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 (London, England : 1993). 15: 535-43. PMID 17502099 DOI: 10.1016/J.Str.2007.03.012  0.299
2007 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 Research. 35: W393-7. PMID 17478513 DOI: 10.1093/Nar/Gkm236  0.441
2007 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: 674-83. PMID 17437410 DOI: 10.1111/J.1528-1167.2007.00926.X  0.646
2007 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, et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Research. 67: 1494-501. PMID 17308087 DOI: 10.1158/0008-5472.Can-06-3297  0.331
2007 Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A. Functional impact of missense variants in BRCA1 predicted by supervised learning. Plos Computational Biology. 3: e26. PMID 17305420 DOI: 10.1371/Journal.Pcbi.0030026  0.316
2007 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: 1059-79. PMID 17170095 DOI: 10.1210/En.2006-0683  0.292
2007 Serysheva I, Ludtke S, Baker M, Cong Y, Topf M, Sali A, Hamilton S, Chiu W. Single Particle Cryo-EM of RyR1 Channel at Subnanometer Resolution Microscopy and Microanalysis. 13. DOI: 10.1017/S1431927607071401  0.773
2006 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 / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 5.6. PMID 18428767 DOI: 10.1002/0471250953.Bi0506S15  0.456
2006 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 Computational Biology. 2: e153. PMID 17096593 DOI: 10.1371/Journal.Pcbi.0020153  0.417
2006 Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Science : a Publication of the Protein Society. 15: 2507-24. PMID 17075131 DOI: 10.1110/Ps.062416606  0.33
2006 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. Journal of Molecular Biology. 363: 835-57. PMID 16982067 DOI: 10.1016/J.Jmb.2006.08.035  0.348
2006 Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function Protein Science. 15: 2366-2380. PMID 16963645 DOI: 10.1110/Ps.062247506  0.394
2006 Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, et al. Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules Structure. 14: 1211-1217. PMID 16955948 DOI: 10.1016/J.Str.2006.06.005  0.809
2006 Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. A composite score for predicting errors in protein structure models. Protein Science : a Publication of the Protein Society. 15: 1653-66. PMID 16751606 DOI: 10.1110/Ps.062095806  0.384
2006 Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. Protein complex compositions predicted by structural similarity. Nucleic Acids Research. 34: 2943-52. PMID 16738133 DOI: 10.1093/Nar/Gkl353  0.428
2006 Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP. Protease accessibility laddering: a proteomic tool for probing protein structure. Structure (London, England : 1993). 14: 653-60. PMID 16615907 DOI: 10.1016/J.Str.2006.02.006  0.398
2006 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. Pharmacological Reviews. 58: 1-2. PMID 16507877 DOI: 10.1124/Pr.58.1.1  0.648
2006 Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting Journal of Molecular Biology. 357: 1655-1668. PMID 16490207 DOI: 10.1016/J.Jmb.2006.01.062  0.824
2006 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. Proceedings of the National Academy of Sciences of the United States of America. 103: 2172-7. PMID 16461911 DOI: 10.1073/Pnas.0506345103  0.353
2006 Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. Variable gap penalty for protein sequence-structure alignment. Protein Engineering, Design & Selection : Peds. 19: 129-33. PMID 16423846 DOI: 10.1093/Protein/Gzj005  0.768
2006 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 Research. 34: D291-5. PMID 16381869 DOI: 10.1093/nar/gkj059  0.747
2005 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, et al. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. Journal of Structural and Functional Genomics. 6: 225-32. PMID 16211523 DOI: 10.1007/S10969-005-6827-0  0.682
2005 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: 886-92. PMID 16170324 DOI: 10.1038/Nsmb992  0.303
2005 Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Current Opinion in Structural Biology. 15: 578-85. PMID 16118050 DOI: 10.1016/J.Sbi.2005.08.001  0.717
2005 Korkin D, Davis FP, Sali A. Localization of protein-binding sites within families of proteins. Protein Science : a Publication of the Protein Society. 14: 2350-60. PMID 16081657 DOI: 10.1110/Ps.051571905  0.376
2005 Dvořák J, Delcroix M, Rossi A, Vopálenský V, Pospíšek M, Šedinová M, Mikeš L, Sajid M, Sali A, McKerrow JH, Horák P, Caffrey CR. Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: Identification, characterisation and putative role in migration and nutrition International Journal For Parasitology. 35: 895-910. PMID 15950230 DOI: 10.1016/J.Ijpara.2005.02.018  0.288
2005 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 (Oxford, England). 21: 2814-20. PMID 15827081 DOI: 10.1093/Bioinformatics/Bti442  0.657
2005 Alber F, Kim MF, Sali A. Structural Characterization of Assemblies from Overall Shape and Subcomplex Compositions Structure. 13: 435-445. PMID 15766545 DOI: 10.1016/J.Str.2005.01.013  0.324
2005 Karchin R, Kelly L, Sali A. Improving functional annotation of no n-s yno no mo us s nps with information theory Proceedings of the Pacific Symposium On Biocomputing 2005, Psb 2005. 397-408. PMID 15759645  0.686
2005 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: 3893-901. PMID 15701722 DOI: 10.1182/Blood-2003-10-3501  0.273
2005 Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy Journal of Structural Biology. 149: 191-203. PMID 15681235 DOI: 10.1016/J.Jsb.2004.11.004  0.822
2005 Sali A, Topf M, Baker ML, Chiu W. Structure of protein assemblies by comparative modeling and electron microscopy Acta Crystallographica Section a Foundations of Crystallography. 61: c3-c3. DOI: 10.1107/S0108767305099897  0.775
2005 Sali A, Chiu W. Macromolecular assemblies highlighted Structure. 13: 339-341. DOI: 10.1016/J.Str.2005.02.010  0.516
2004 Maurer SM, Rai A, Sali A. Finding cures for tropical diseases: is open source an answer? Plos Medicine. 1: e56. PMID 15630466 DOI: 10.1371/Journal.Pmed.0010056  0.253
2004 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 Biology. 2: e380. PMID 15523559 DOI: 10.1371/Journal.Pbio.0020380  0.322
2004 Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Current Opinion in Structural Biology. 14: 313-24. PMID 15193311 DOI: 10.1016/J.Sbi.2004.04.006  0.753
2004 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 Research. 64: 3790-7. PMID 15172985 DOI: 10.1158/0008-5472.Can-03-3009  0.282
2004 John B, Sali A. Detection of homologous proteins by an intermediate sequence search. Protein Science : a Publication of the Protein Society. 13: 54-62. PMID 14691221 DOI: 10.1110/Ps.03335004  0.266
2004 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 Research. 32: D217-22. PMID 14681398 DOI: 10.1093/nar/gkh095  0.459
2004 Jacobson M, Sali A. Comparative Protein Structure Modeling and its Applications to Drug Discovery Annual Reports in Medicinal Chemistry. 39: 259-276. DOI: 10.1016/S0065-7743(04)39020-2  0.586
2003 Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods in Enzymology. 374: 461-491. PMID 14696385 DOI: 10.1016/S0076-6879(03)74020-8  0.456
2003 John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Research. 31: 3982-92. PMID 12853614 DOI: 10.1093/Nar/Gkg460  0.266
2003 Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Martí-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis Nucleic Acids Research. 31: 3375-3380. PMID 12824331 DOI: 10.1093/Nar/Gkg543  0.432
2003 Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Research. 31: 3311-5. PMID 12824315 DOI: 10.1093/Nar/Gkg619  0.407
2003 Gao H, 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. PMID 12809609 DOI: 10.1016/S0092-8674(03)00427-6  0.502
2003 Lee SA, Shen EL, Fiser A, Sali A, Guo S. The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons. Development (Cambridge, England). 130: 2669-79. PMID 12736211 DOI: 10.1242/Dev.00502  0.248
2003 Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics Nature. 422: 216-225. PMID 12634795 DOI: 10.1038/Nature01513  0.386
2003 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. PMID 12499313 DOI: 10.1093/Bioinformatics/19.1.165  0.396
2003 Marti-Renom MA, Madhusudhan MS, Eswar N, Pieper U, Shen M, Sali A, Fiser A, Mirkovic N, John B, Stuart A. Modeling Protein Structure from its Sequence Current Protocols in Human Genetics. 3. DOI: 10.1002/0471250953.Bi0501S03  0.46
2002 Iverson GM, Reddel S, Victoria EJ, Cockerill KA, Wang Y, Marti-Renom MA, Sali A, Marquis DM, Krilis SA, Linnik MD. Use of Single Point Mutations in Domain I of β2-Glycoprotein I to Determine Fine Antigenic Specificity of Antiphospholipid Autoantibodies Journal of Immunology. 169: 7097-7103. PMID 12471146 DOI: 10.4049/Jimmunol.169.12.7097  0.276
2002 Fiser A, Feig M, Brooks CL, Sali A. Evolution and physics in comparative protein structure modeling. Accounts of Chemical Research. 35: 413-21. PMID 12069626 DOI: 10.1021/Ar010061H  0.589
2002 Vernal J, Fiser A, Sali A, Müller M, Cazzulo JJ, Nowicki C. Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis. Biochemical and Biophysical Research Communications. 293: 633-9. PMID 12054650 DOI: 10.1016/S0006-291X(02)00270-X  0.287
2002 Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 10: 435-440. PMID 12005441 DOI: 10.1016/S0969-2126(02)00731-1  0.402
2002 Yang Y, Li L, 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. The Journal of Biological Chemistry. 277: 25756-74. PMID 11956218 DOI: 10.1074/Jbc.M202575200  0.298
2002 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 G, Huang R, Ilyin V, et al. Structural genomics: a pipeline for providing structures for the biologist. Protein Science : a Publication of the Protein Society. 11: 723-38. PMID 11910018 DOI: 10.1110/Ps.4570102  0.681
2002 Stuart AC, Ilyin VA, Sali A. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics (Oxford, England). 18: 200-1. PMID 11836232 DOI: 10.1093/Bioinformatics/18.1.200  0.266
2002 Melo F, Sánchez R, Sali A. Statistical potentials for fold assessment. Protein Science : a Publication of the Protein Society. 11: 430-48. PMID 11790853 DOI: 10.1002/Pro.110430  0.775
2002 Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research. 30: 255-9. PMID 11752309 DOI: 10.1093/Nar/30.1.255  0.266
2002 Sali A, Eswar N, Pieper U, Marti-Renom MA, Madhusudhan M, Fiser A, Ilyin V. Comparative protein structure modeling of genes and genomes Acta Crystallographica Section a Foundations of Crystallography. 58: c49-c49. DOI: 10.1146/Annurev.Biophys.29.1.291  0.775
2002 Sali A, Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B. Reply to Moult et al. Structure. 10: 292-293. DOI: 10.1016/S0969-2126(02)00729-3  0.373
2002 Marti-Renom MA, Yerkovich B, Sali A. Comparative Protein Structure Prediction Current Protocols in Protein Science. 28. DOI: 10.1002/0471140864.Ps0209S28  0.464
2001 Eyrich VA, Martí-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 (Oxford, England). 17: 1242-3. PMID 11751240 DOI: 10.1093/Bioinformatics/17.12.1242  0.407
2001 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: 373-86. PMID 11701127 DOI: 10.1016/S0092-8674(01)00539-6  0.475
2001 Beckmann R, Spahn CM, 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: 361-72. PMID 11701126 DOI: 10.1016/S0092-8674(01)00541-4  0.484
2001 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. Proceedings of the National Academy of Sciences of the United States of America. 98: 12896-901. PMID 11698677 DOI: 10.1073/Pnas.181466998  0.567
2001 Wong GW, Yasuda S, Madhusudhan MS, Li L, Yang Y, Krilis SA, Šali A, Stevens RL. Human Tryptase ε (PRSS22), a New Member of the Chromosome 16p13.3 Family of Human Serine Proteases Expressed in Airway Epithelial Cells Journal of Biological Chemistry. 276: 49169-49182. PMID 11602603 DOI: 10.1074/Jbc.M108677200  0.29
2001 Baker D, Sali A. Protein Structure Prediction and Structural Genomics Science. 294: 93-96. PMID 11588250 DOI: 10.1126/Science.1065659  0.334
2001 Martí-Renom MA, Ilyin VA, Sali A. DBAli: a database of protein structure alignments Bioinformatics. 17: 746-747. PMID 11524379 DOI: 10.1093/Bioinformatics/17.8.746  0.377
2001 Barrientos LG, Campos-Olivas R, Louis JM, Fiser A, Šali A, Gronenborn AM. 1H, 13N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N [6] Journal of Biomolecular Nmr. 19: 289-290. PMID 11330821 DOI: 10.1023/A:1011292919947  0.266
2001 Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Eduardo Fajardo J, Eswar N, Sanchez R, Sali A, Gaasterland T. Homology-based annotation yields 1,042 new candidate genes in the drosophila melanogaster genome Nature Genetics. 27: 337-340. PMID 11242120 DOI: 10.1038/85922  0.747
2001 Sánchez R, Sali A. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods in Molecular Biology (Clifton, N.J.). 143: 97-129. PMID 11084904 DOI: 10.1385/1-59259-368-2:97  0.725
2001 Groft CM, Beckmann R, Sali A, Burley SK. Nature Structural Biology. 8: 745-745. DOI: 10.1038/Nsb0901-745  0.489
2000 Sánchez R, Pieper U, Melo F, Eswar N, Martí-Renom MA, Madhusudhan MS, Mirković N, Sali A. Protein structure modeling for structural genomics. Nature Structural Biology. 986-90. PMID 11104007 DOI: 10.1038/80776  0.725
2000 Groft CM, Beckmann R, Sali A, Burley SK. Crystal structures of ribosome anti-association factor IF6. Nature Structural Biology. 7: 1156-64. PMID 11101899 DOI: 10.1038/82017  0.53
2000 Liedtke W, Choe Y, Martí-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: 525-35. PMID 11081638 DOI: 10.1016/S0092-8674(00)00143-4  0.238
2000 Fiser A, Do RKG, Šali A. Modeling of loops in protein structures. Protein Science. 9: 1753-1773. PMID 11045621 DOI: 10.1110/Ps.9.9.1753  0.365
2000 Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure. 29: 291-325. PMID 10940251 DOI: 10.1146/annurev.biophys.29.1.291  0.444
2000 Wu G, McArthur AG, Fiser A, Šali A, Sogin ML, Müller M. Core histones of the amitochondriate protist, Giardia lamblia Molecular Biology and Evolution. 17: 1156-1163. PMID 10908635 DOI: 10.1093/Oxfordjournals.Molbev.A026398  0.296
2000 Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends in Biochemical Sciences. 25: 331-9. PMID 10871884 DOI: 10.1016/S0968-0004(00)01610-8  0.686
2000 Jin S, 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. Proceedings of the National Academy of Sciences of the United States of America. 97: 7301-6. PMID 10860994 DOI: 10.1073/Pnas.97.13.7301  0.256
2000 Sánchez R, Pieper U, Mirković N, de Bakker PI, Wittenstein E, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research. 28: 250-3. PMID 10592238 DOI: 10.1093/nar/28.1.250  0.407
1999 Sánchez R, S̆ali A. ModBase: a database of comparative protein structure models. Bioinformatics. 15: 1060-1061. PMID 10745998 DOI: 10.1093/Bioinformatics/15.12.1060  0.786
1999 Sali A, Kuriyan J. Challenges at the frontiers of structural biology. Trends in Cell Biology. 9: M20-4. PMID 10611675 DOI: 10.1016/S0968-0004(99)01494-2  0.619
1999 Wong GW, Tang Y, Feyfant E, Šali 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 Journal of Biological Chemistry. 274: 30784-30793. PMID 10521469 DOI: 10.1074/Jbc.274.43.30784  0.27
1999 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. Nature Genetics. 23: 151-7. PMID 10508510 DOI: 10.1038/13783  0.649
1999 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. Nature Structural Biology. 6: 615-9. PMID 10404214 DOI: 10.1038/10658  0.266
1999 Miwa JM, Ibanez-Tallon I, Crabtree GW, Sánchez R, Sali A, Role LW, Heintz N. lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS. Neuron. 23: 105-14. PMID 10402197 DOI: 10.1016/S0896-6273(00)80757-6  0.766
1999 Wu G, Fiser A, ter Kuile B, Sali A, Müller M. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proceedings of the National Academy of Sciences of the United States of America. 96: 6285-90. PMID 10339579 DOI: 10.1073/Pnas.96.11.6285  0.266
1999 Sánchez R, Šali A. Comparative Protein Structure Modeling in Genomics Journal of Computational Physics. 151: 388-401. DOI: 10.1006/Jcph.1999.6200  0.787
1998 Dobson CM, Šali A, Karplus M. Protein Folding: A Perspective from Theory and Experiment. Angewandte Chemie (International Ed. in English). 37: 868-893. PMID 29711488 DOI: 10.1002/(Sici)1521-3773(19980420)37:7<868::Aid-Anie868>3.0.Co;2-H  0.54
1998 Sali A. 100,000 protein structures for the biologist. Nature Structural Biology. 5: 1029-32. PMID 9846869 DOI: 10.1038/4136  0.266
1998 Sánchez R, Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proceedings of the National Academy of Sciences of the United States of America. 95: 13597-602. PMID 9811845 DOI: 10.1073/Pnas.95.23.13597  0.725
1998 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: 439-49. PMID 9727487 DOI: 10.1016/S0092-8674(00)81585-8  0.528
1998 Huang C, Šali A, Stevens RL. Regulation and function of mast cell proteases in inflammation. Journal of Clinical Immunology. 18: 169-183. PMID 9624576 DOI: 10.1023/A:1020574820797  0.276
1998 Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI. Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition The Journal of Chemical Physics. 108: 6466-6483. DOI: 10.1063/1.476053  0.54
1998 Dobson C, Šali A, Karplus M. Proteinfaltung aus theoretischer und experimenteller Sicht Angewandte Chemie. 110: 908-935. DOI: 10.1002/(Sici)1521-3757(19980403)110:7<908::Aid-Ange908>3.0.Co;2-0  0.483
1997 Sánchez R, Sali A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins. 50-8. PMID 9485495 DOI: 10.1002/(sici)1097-0134(1997)1+<50::aid-prot8>3.3.co;2-w  0.411
1997 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: 335-45. PMID 9363942 DOI: 10.1016/S0092-8674(00)80417-1  0.543
1997 Russel M, Linderoth NA, Sali A. Filamentous phage assembly: variation on a protein export theme. Gene. 192: 23-32. PMID 9224870 DOI: 10.1016/S0378-1119(96)00801-3  0.266
1997 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. Microbial Drug Resistance (Larchmont, N.Y.). 2: 277-86. PMID 9158773 DOI: 10.1089/mdr.1996.2.277  0.266
1997 Sánchez R, Sali A. Advances in comparative protein-structure modelling. Current Opinion in Structural Biology. 7: 206-14. PMID 9094331 DOI: 10.1016/S0959-440X(97)80027-9  0.725
1997 Koulich D, Orlova M, Malhotra A, Sali A, Darst SA, Borukhov S. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. The Journal of Biological Chemistry. 272: 7201-10. PMID 9054416 DOI: 10.1074/Jbc.272.11.7201  0.306
1997 Sánchez R, Šali A. Comparative protein structure modeling as an optimization problem Journal of Molecular Structure-Theochem. 489-496. DOI: 10.1016/S0166-1280(96)04971-8  0.79
1997 Sánchez R, Šali A. Evaluation of comparative protein structure modeling by MODELLER-3 Proteins: Structure, Function, and Genetics. 29: 50-58. DOI: 10.1002/(Sici)1097-0134(1997)1+<50::Aid-Prot8>3.0.Co;2-S  0.766
1996 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. Journal of Experimental Medicine. 184: 1061-1073. PMID 9064323 DOI: 10.1084/Jem.184.3.1061  0.299
1996 Xu LZ, Sánchez R, Sali A, Heintz N. Ligand specificity of brain lipid-binding protein. The Journal of Biological Chemistry. 271: 24711-9. PMID 8798739 DOI: 10.1074/Jbc.271.40.24711  0.732
1996 Dinner AR, Sali A, Karplus M. The folding mechanism of larger model proteins: role of native structure. Proceedings of the National Academy of Sciences of the United States of America. 93: 8356-61. PMID 8710875 DOI: 10.1073/Pnas.93.16.8356  0.704
1996 Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins. 23: 318-26. PMID 8710825 DOI: 10.1002/Prot.340230306  0.72
1995 Sali A. Comparative protein modeling by satisfaction of spatial restraints. Molecular Medicine Today. 1: 270-7. PMID 9415161 DOI: 10.1016/s1357-4310(95)91170-7  0.453
1995 Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Current Opinion in Structural Biology. 5: 58-73. PMID 7773748 DOI: 10.1016/0959-440X(95)80010-X  0.532
1995 Wu X, 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 N-terminal SH3 domain of c-Crk. Structure (London, England : 1993). 3: 215-26. PMID 7735837 DOI: 10.1016/S0969-2126(01)00151-4  0.662
1995 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. The Journal of Biological Chemistry. 270: 19524-31. PMID 7642636 DOI: 10.1074/Jbc.270.33.19524  0.532
1995 Šali A. Modelling mutations and homologous proteins Current Opinion in Biotechnology. 6: 437-451. PMID 7579655 DOI: 10.1016/0958-1669(95)80074-3  0.45
1994 Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology. 234: 779-815. PMID 8254673 DOI: 10.1006/Jmbi.1993.1626  0.452
1994 Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. Journal of Molecular Biology. 235: 1614-36. PMID 8107095 DOI: 10.1006/Jmbi.1994.1110  0.532
1994 Sali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Science : a Publication of the Protein Society. 3: 1582-96. PMID 7833817 DOI: 10.1002/Pro.5560030923  0.668
1994 Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 369: 248-51. PMID 7710478 DOI: 10.1038/369248A0  0.532
1994 Dinner A, Šali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations The Journal of Chemical Physics. 101: 1444-1451. DOI: 10.1063/1.467769  0.697
1993 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. Biochemical Society Transactions. 21: 597-604. PMID 8224474 DOI: 10.1042/Bst0210597  0.644
1992 Zhu ZY, Sali A, Blundell TL. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Engineering. 5: 43-51. PMID 1631045 DOI: 10.1093/Protein/5.1.43  0.452
1992 Sali A, Veerapandian B, Cooper JB, Moss DS, Hofmann T, Blundell TL. Domain flexibility in aspartic proteinases. Proteins. 12: 158-70. PMID 1603805 DOI: 10.1002/Prot.340120209  0.452
1992 Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Science : a Publication of the Protein Society. 1: 216-26. PMID 1304904 DOI: 10.1002/Pro.5560010203  0.703
1990 Sali A, Overington JP, Johnson MS, Blundell TL. From comparisons of protein sequences and structures to protein modelling and design. Trends in Biochemical Sciences. 15: 235-40. PMID 2200167 DOI: 10.1016/0968-0004(90)90036-B  0.713
1990 Johnson MS, Sali A, Blundell TL. Phylogenetic relationships from three-dimensional protein structures. Methods in Enzymology. 183: 670-90. PMID 2156133 DOI: 10.1016/0076-6879(90)83044-A  0.551
1990 Overington J, Johnson MS, Sali A, Blundell TL. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proceedings. Biological Sciences / the Royal Society. 241: 132-45. PMID 1978340 DOI: 10.1098/Rspb.1990.0077  0.694
1990 Johnson M, Overington J, Šali A, Thomas P, Blundell T. From the comparative analysis of proteins to knowledge based modeling Journal of Molecular Graphics. 8: 231. DOI: 10.1016/0263-7855(90)80017-A  0.574
1989 Sali A, Veerapandian B, Cooper J, Foundling S, Hoover D, Blundell T. 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. The Embo Journal. 8: 2179-2188. DOI: 10.1002/J.1460-2075.1989.Tb08340.X  0.48
1987 Šali A, Turk V. Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases. Biological Chemistry Hoppe-Seyler. 368: 493-500. PMID 3497644 DOI: 10.1515/Bchm3.1987.368.1.493  0.408
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