Year |
Citation |
Score |
2024 |
Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, A M J J Bonvin A, DiMaio F, ... ... Sali A, et al. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology. 168546. PMID 38508301 DOI: 10.1016/j.jmb.2024.168546 |
0.302 |
|
2024 |
Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. Integrative spatiotemporal map of nucleocytoplasmic transport. Biorxiv : the Preprint Server For Biology. PMID 38260487 DOI: 10.1101/2023.12.31.573409 |
0.508 |
|
2023 |
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, ... ... Sali A, et al. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature. PMID 38096902 DOI: 10.1038/s41586-023-06947-z |
0.583 |
|
2023 |
Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, ... ... Sali A, et al. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. Journal of Molecular Biology. 168021. PMID 36828268 DOI: 10.1016/j.jmb.2023.168021 |
0.603 |
|
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 |
0.305 |
|
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 |
0.317 |
|
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 |
0.32 |
|
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 |
0.38 |
|
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 |
0.345 |
|
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 |
0.301 |
|
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 |
0.551 |
|
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 |
0.415 |
|
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 |
0.434 |
|
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 |
0.653 |
|
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 |
0.535 |
|
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 |
0.433 |
|
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 |
0.411 |
|
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 |
0.378 |
|
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 |
0.308 |
|
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 |
0.392 |
|
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 |
0.349 |
|
2019 |
Axen SD, Clancy B, Salafsky J, Sali A. Modeling Conformational Changes in Proteins Based on Second Harmonic Generation Data Biophysical Journal. 116: 334a. DOI: 10.1016/J.Bpj.2018.11.1820 |
0.367 |
|
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 |
0.377 |
|
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 |
0.555 |
|
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 |
0.38 |
|
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 |
0.308 |
|
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 |
0.397 |
|
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 |
0.329 |
|
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 |
0.38 |
|
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 |
0.381 |
|
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 |
0.558 |
|
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 |
0.43 |
|
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 |
0.403 |
|
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 |
0.326 |
|
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 |
0.338 |
|
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 |
0.38 |
|
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 |
0.415 |
|
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 |
0.316 |
|
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 |
0.316 |
|
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 |
0.417 |
|
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 |
0.345 |
|
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 |
0.368 |
|
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 |
0.325 |
|
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 |
0.419 |
|
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 |
0.361 |
|
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 |
0.563 |
|
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 |
0.317 |
|
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 |
0.54 |
|
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 |
0.311 |
|
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 |
0.309 |
|
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 |
0.36 |
|
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 |
0.353 |
|
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 |
0.307 |
|
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 |
0.353 |
|
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 |
0.407 |
|
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 |
0.74 |
|
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 |
0.544 |
|
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 |
0.428 |
|
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 |
0.381 |
|
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 |
0.317 |
|
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 |
0.422 |
|
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 |
0.357 |
|
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 |
0.328 |
|
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 |
0.375 |
|
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 |
0.3 |
|
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 |
0.402 |
|
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 |
0.399 |
|
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 |
0.348 |
|
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 |
0.61 |
|
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 |
0.365 |
|
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 |
0.327 |
|
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 |
0.381 |
|
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 |
0.303 |
|
2014 |
Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, CimermanÄiÄ 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 |
0.355 |
|
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 |
0.402 |
|
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 |
0.341 |
|
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 |
0.407 |
|
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 |
0.435 |
|
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 |
0.316 |
|
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 |
0.574 |
|
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 |
0.364 |
|
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 |
0.38 |
|
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 |
0.487 |
|
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 |
0.323 |
|
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 |
0.308 |
|
2014 |
Politis A, Schmidt C, Tjioe E, Sali A, Robinson CV. Determining the 3D Topologies of Heteromeric Protein Assemblies by a Mass-Spectrometry Based Hybrid Approach Biophysical Journal. 106: 466a. DOI: 10.1016/J.Bpj.2013.11.2640 |
0.36 |
|
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 |
0.395 |
|
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 |
0.571 |
|
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 |
0.357 |
|
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 |
0.366 |
|
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 |
0.386 |
|
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 |
0.401 |
|
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 |
0.337 |
|
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 |
0.398 |
|
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 |
0.352 |
|
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 |
0.365 |
|
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 |
0.356 |
|
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 |
0.315 |
|
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 |
0.365 |
|
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 |
0.328 |
|
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 |
0.334 |
|
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 |
0.39 |
|
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 |
0.392 |
|
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 |
0.461 |
|
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 |
0.416 |
|
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 |
0.4 |
|
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 |
0.355 |
|
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 |
0.346 |
|
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 |
0.363 |
|
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 |
0.463 |
|
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 |
0.602 |
|
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 |
0.341 |
|
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 |
0.367 |
|
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 |
0.444 |
|
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 |
0.342 |
|
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 |
0.459 |
|
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 |
0.428 |
|
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 |
0.421 |
|
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 |
0.369 |
|
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 |
0.372 |
|
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 |
0.388 |
|
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 |
0.385 |
|
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 |
0.383 |
|
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 |
0.301 |
|
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 |
0.303 |
|
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 |
0.35 |
|
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 |
0.383 |
|
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 |
0.378 |
|
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 |
0.421 |
|
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 |
0.396 |
|
2011 |
Lima C, Sali A, Kostic M. Structure meets the membrane. Structure (London, England : 1993). 19: 1347. PMID 22000504 DOI: 10.1016/J.Str.2011.09.009 |
0.367 |
|
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 |
0.586 |
|
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 |
0.374 |
|
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 |
0.328 |
|
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 |
0.431 |
|
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 |
0.367 |
|
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 |
0.333 |
|
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 |
0.328 |
|
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 |
0.384 |
|
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 |
0.368 |
|
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 |
0.437 |
|
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 |
0.63 |
|
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 |
0.403 |
|
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 |
0.66 |
|
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 |
0.351 |
|
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 |
0.423 |
|
2010 |
Schneidman-Duhovny D, Hammel M, Sali A. FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Research. 38: W540-4. PMID 20507903 DOI: 10.1093/Nar/Gkq461 |
0.351 |
|
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 |
0.36 |
|
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 |
0.409 |
|
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 |
0.371 |
|
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 |
0.415 |
|
2010 |
Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. Plos Computational Biology. 6: e1000668. PMID 20140189 DOI: 10.1371/Journal.Pcbi.1000668 |
0.42 |
|
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 |
0.67 |
|
2010 |
Schlessinger A, Sali A. Classification of Human Solute Carrier Superfamily Members Reveals Functional Similarities across Families Biophysical Journal. 98: 684a. DOI: 10.1016/J.Bpj.2009.12.3757 |
0.356 |
|
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 |
0.344 |
|
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 |
0.45 |
|
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 |
0.639 |
|
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 |
0.417 |
|
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 |
0.688 |
|
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 |
0.377 |
|
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 |
0.463 |
|
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 |
0.301 |
|
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 |
0.337 |
|
2009 |
Pandey KC, Barkan DT, Sali A, Rosenthal PJ. Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. Plos One. 4: e5694. PMID 19479029 DOI: 10.1371/Journal.Pone.0005694 |
0.333 |
|
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 |
0.423 |
|
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 |
0.411 |
|
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 |
0.626 |
|
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 |
0.777 |
|
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 |
0.786 |
|
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 |
0.406 |
|
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 |
0.688 |
|
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 |
0.692 |
|
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 |
0.72 |
|
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 |
0.432 |
|
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 |
0.326 |
|
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 |
0.573 |
|
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 |
0.409 |
|
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 |
0.346 |
|
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 |
0.49 |
|
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 |
0.582 |
|
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 |
0.481 |
|
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 |
0.625 |
|
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 |
0.389 |
|
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 |
0.357 |
|
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 |
0.673 |
|
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 |
0.641 |
|
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 |
0.638 |
|
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 |
0.33 |
|
2008 |
Robinson CV, Sali A, Baumeister W. The molecular sociology of the cell. Nature. 450: 973-82. PMID 18075576 DOI: 10.1038/Nature06523 |
0.396 |
|
2008 |
Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. Plos Computational Biology. 3: e241. PMID 18069886 DOI: 10.1371/Journal.Pcbi.0030241 |
0.367 |
|
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 |
0.574 |
|
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 |
0.485 |
|
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 |
0.439 |
|
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 |
0.388 |
|
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 |
0.412 |
|
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 |
0.649 |
|
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 |
0.333 |
|
2007 |
Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. Characterization of protein hubs by inferring interacting motifs from protein interactions. Plos Computational Biology. 3: 1761-71. PMID 17941705 DOI: 10.1371/Journal.Pcbi.0030178 |
0.373 |
|
2007 |
Melo F, Sali A. Fold assessment for comparative protein structure modeling Protein Science. 16: 2412-2426. PMID 17905832 DOI: 10.1110/Ps.072895107 |
0.387 |
|
2007 |
Feyfant E, Sali A, Fiser A. Modeling mutations in protein structures Protein Science. 16: 2030-2041. PMID 17766392 DOI: 10.1110/Ps.072855507 |
0.377 |
|
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 |
0.448 |
|
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 |
0.323 |
|
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 |
0.44 |
|
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 |
0.621 |
|
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 |
0.322 |
|
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 |
0.307 |
|
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 |
0.521 |
|
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 |
0.483 |
|
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 |
0.456 |
|
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 |
0.458 |
|
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 |
0.384 |
|
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 |
0.339 |
|
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 |
0.605 |
|
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 |
0.392 |
|
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 |
0.429 |
|
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 |
0.444 |
|
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 |
0.629 |
|
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 |
0.665 |
|
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 |
0.409 |
|
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 |
0.649 |
|
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 |
0.73 |
|
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 |
0.41 |
|
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 |
0.347 |
|
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 |
0.615 |
|
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 |
0.379 |
|
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 |
0.306 |
|
2005 |
Espadaler J, Aragüés R, Eswar N, Marti-Renom MA, Querol E, Avilés FX, Sali A, Oliva B. Detecting remotely related proteins by their interactions and sequence similarity. Proceedings of the National Academy of Sciences of the United States of America. 102: 7151-6. PMID 15883372 DOI: 10.1073/Pnas.0500831102 |
0.412 |
|
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 |
0.626 |
|
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 |
0.355 |
|
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 |
0.626 |
|
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 |
0.661 |
|
2005 |
Davis FP, Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics (Oxford, England). 21: 1901-7. PMID 15657096 DOI: 10.1093/Bioinformatics/Bti277 |
0.446 |
|
2005 |
Rossi A, Deveraux Q, Turk B, Sali A. Comprehensive search for cysteine cathepsins in the human genome. Biological Chemistry. 385: 363-72. PMID 15195995 DOI: 10.1515/Bc.2004.040 |
0.31 |
|
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 |
0.644 |
|
2005 |
Sali A, Chiu W. Macromolecular assemblies highlighted Structure. 13: 339-341. DOI: 10.1016/J.Str.2005.02.010 |
0.368 |
|
2005 |
Shen M, Davis FP, Sali A. The optimal size of a globular protein domain: A simple sphere-packing model Chemical Physics Letters. 405: 224-228. DOI: 10.1016/J.Cplett.2005.02.029 |
0.375 |
|
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 |
Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. High-throughput computational and experimental techniques in structural genomics. Genome Research. 14: 2145-54. PMID 15489337 DOI: 10.1101/Gr.2537904 |
0.463 |
|
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 |
0.664 |
|
2004 |
Marti-Renom MA, Madhusudhan MS, Sali A. Alignment of protein sequences by their profiles. Protein Science : a Publication of the Protein Society. 13: 1071-87. PMID 15044736 DOI: 10.1110/Ps.03379804 |
0.382 |
|
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 |
0.335 |
|
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 |
0.396 |
|
2004 |
Fiser A, Sali A. ModLoop: automated modeling of loops in protein structures. Bioinformatics (Oxford, England). 19: 2500-1. PMID 14668246 DOI: 10.1093/Bioinformatics/Btg362 |
0.451 |
|
2004 |
Sali A. NIH workshop on structural proteomics of biological complexes. Structure (London, England : 1993). 11: 1043-7. PMID 12962622 DOI: 10.1016/S0969-2126(03)00163-1 |
0.374 |
|
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 |
0.634 |
|
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 |
0.485 |
|
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 |
0.436 |
|
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 |
0.462 |
|
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 |
0.389 |
|
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 |
0.37 |
|
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 |
0.397 |
|
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 |
0.416 |
|
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 |
0.493 |
|
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 |
0.597 |
|
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 |
0.4 |
|
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 |
0.315 |
|
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 |
0.394 |
|
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 |
0.425 |
|
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 |
0.638 |
|
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 |
0.487 |
|
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 |
0.475 |
|
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 |
0.344 |
|
2002 |
Marti-Renom MA, Yerkovich B, Sali A. Comparative Protein Structure Prediction Current Protocols in Protein Science. 28. DOI: 10.1002/0471140864.Ps0209S28 |
0.496 |
|
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 |
0.395 |
|
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 |
0.391 |
|
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 |
0.352 |
|
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 |
0.414 |
|
2001 |
Baker D, Sali A. Protein Structure Prediction and Structural Genomics Science. 294: 93-96. PMID 11588250 DOI: 10.1126/Science.1065659 |
0.472 |
|
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 |
0.422 |
|
2001 |
Wong GW, Li L, Madhusudhan MS, Krilis SA, Gurish MF, Rothenberg ME, Sali A, Stevens RL. Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases. The Journal of Biological Chemistry. 276: 20648-58. PMID 11259427 DOI: 10.1074/Jbc.M010422200 |
0.335 |
|
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 |
0.608 |
|
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 |
0.665 |
|
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 |
0.683 |
|
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 |
0.398 |
|
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 |
0.384 |
|
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 |
0.378 |
|
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 |
0.321 |
|
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 |
0.64 |
|
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 |
0.306 |
|
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 |
0.342 |
|
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 |
0.658 |
|
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 |
0.581 |
|
1999 |
Sali A. Functional links between proteins. Nature. 402: 23, 25-6. PMID 10573411 DOI: 10.1038/46915 |
0.412 |
|
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 |
0.337 |
|
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 |
0.319 |
|
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 |
0.545 |
|
1999 |
Burge C, Sali A, Borodovsky M. The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11–14, 1999, Atlanta, Georgia, USA) Bioinformatics. 15: 865-866. DOI: 10.1093/Bioinformatics/15.11.865 |
0.344 |
|
1999 |
Sánchez R, Šali A. Comparative Protein Structure Modeling in Genomics Journal of Computational Physics. 151: 388-401. DOI: 10.1006/Jcph.1999.6200 |
0.697 |
|
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 |
0.455 |
|
1998 |
Sali A. 100,000 protein structures for the biologist. Nature Structural Biology. 5: 1029-32. PMID 9846869 DOI: 10.1038/4136 |
0.486 |
|
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 |
0.684 |
|
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 |
0.332 |
|
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 |
0.468 |
|
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 |
0.355 |
|
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 |
0.329 |
|
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 |
0.548 |
|
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 |
0.37 |
|
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 |
0.701 |
|
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 |
0.32 |
|
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 |
0.685 |
|
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 |
0.671 |
|
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 |
0.582 |
|
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 |
0.703 |
|
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 |
0.758 |
|
1996 |
Sali A. Comparative protein modeling by satisfaction of spatial restraints Acta Crystallographica Section A. 52: 88-88. DOI: 10.1107/S0108767396095578 |
0.357 |
|
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 |
0.378 |
|
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 |
0.522 |
|
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 |
0.654 |
|
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 |
0.479 |
|
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 |
0.478 |
|
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 |
0.571 |
|
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 |
0.493 |
|
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 |
0.686 |
|
1994 |
Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 369: 248-51. PMID 7710478 DOI: 10.1038/369248A0 |
0.472 |
|
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 |
0.661 |
|
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 |
0.705 |
|
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 |
0.545 |
|
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 |
0.521 |
|
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 |
0.713 |
|
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 |
0.73 |
|
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 |
0.57 |
|
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 |
0.711 |
|
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 |
0.636 |
|
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 |
0.47 |
|
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 |
0.426 |
|
Low-probability matches (unlikely to be authored by this person) |
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 |
0.299 |
|
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 |
0.299 |
|
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 |
0.298 |
|
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 |
0.298 |
|
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 |
0.298 |
|
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 |
0.297 |
|
2009 |
Lezon TR, Sali A, Bahar I. Global motions of the nuclear pore complex: insights from elastic network models. Plos Computational Biology. 5: e1000496. PMID 19730674 DOI: 10.1371/Journal.Pcbi.1000496 |
0.297 |
|
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 |
0.297 |
|
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 |
0.294 |
|
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 |
0.292 |
|
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 |
0.291 |
|
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 |
0.291 |
|
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 |
0.289 |
|
2022 |
Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, ... ... Sali A, et al. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Research. PMID 36420884 DOI: 10.1093/nar/gkac1077 |
0.289 |
|
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 |
0.286 |
|
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 |
0.286 |
|
2022 |
Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, et al. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophysical Reviews. 1-21. PMID 36474933 DOI: 10.1007/s12551-022-01013-w |
0.284 |
|
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 |
0.283 |
|
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 |
0.283 |
|
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 |
0.281 |
|
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 |
0.281 |
|
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 |
0.281 |
|
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 |
0.28 |
|
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 |
0.28 |
|
2008 |
Anderson CM, Korkin D, Smith DL, Makovets S, Seidel JJ, Sali A, Blackburn EH. Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break. Genes & Development. 22: 854-9. PMID 18334620 DOI: 10.1101/Gad.1646208 |
0.279 |
|
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 |
0.277 |
|
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 |
0.275 |
|
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 |
0.275 |
|
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 |
0.274 |
|
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 |
0.274 |
|
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 |
0.272 |
|
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 |
0.272 |
|
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 |
0.271 |
|
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 |
0.27 |
|
2023 |
Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. Acs Central Science. 9: 992-1007. PMID 37252352 DOI: 10.1021/acscentsci.3c00063 |
0.268 |
|
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 |
0.268 |
|
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 |
0.268 |
|
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 |
0.268 |
|
2001 |
Groft CM, Beckmann R, Sali A, Burley SK. Nature Structural Biology. 8: 745-745. DOI: 10.1038/Nsb0901-745 |
0.266 |
|
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 |
0.266 |
|
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 |
0.263 |
|
2023 |
Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Biorxiv : the Preprint Server For Biology. PMID 36747776 DOI: 10.1101/2023.01.27.525930 |
0.263 |
|
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 |
0.263 |
|
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 |
0.262 |
|
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 |
0.262 |
|
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 |
0.262 |
|
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 |
0.26 |
|
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 |
0.258 |
|
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 |
0.256 |
|
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 |
0.255 |
|
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 |
0.255 |
|
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 |
0.254 |
|
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 |
0.254 |
|
2023 |
Hu M, Zhang X, Latham A, Šali A, Ideker T, Lundberg E. Tools for assembling the cell: Towards the era of cell structural bioinformatics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 29: 661-665. PMID 38160316 |
0.253 |
|
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 |
0.251 |
|
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 |
0.25 |
|
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 |
0.249 |
|
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 |
0.248 |
|
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 |
0.248 |
|
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 |
0.247 |
|
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 |
0.246 |
|
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 |
0.246 |
|
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 |
0.245 |
|
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 |
0.245 |
|
1999 |
S̆ali A, Kuriyan J. Challenges at the frontiers of structural biology Trends in Genetics. 15: M20-M24. DOI: 10.1016/S0168-9525(99)01908-3 |
0.244 |
|
1998 |
Kandiah DA, Sali A, Sheng Y, Victoria EJ, Marquis DM, Coutts SM, Krilis SA. Current Insights into the “Antiphospholipid” Syndrome: Clinical, Immunological, and Molecular Aspects Advances in Immunology. 70: 507-563. PMID 9755344 DOI: 10.1016/S0065-2776(08)60393-4 |
0.243 |
|
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 |
0.243 |
|
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 |
0.243 |
|
2001 |
Borodovsky M, Koonin EV, Burge C, Fickett JW, Logsdon J, Sali A, Stormo GD, Zhulin IB. The Third Georgia Tech–Emory International Conference On Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15–18, 2001, Atlanta, Georgia, Usa) Bioinformatics. 17: 859-861. DOI: 10.1093/Bioinformatics/17.10.859 |
0.242 |
|
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 |
0.241 |
|
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 |
0.241 |
|
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 |
0.241 |
|
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 |
0.239 |
|
2023 |
Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nature Structural & Molecular Biology. PMID 36782050 DOI: 10.1038/s41594-022-00918-0 |
0.239 |
|
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 |
0.238 |
|
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 |
0.237 |
|
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 |
0.233 |
|
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 |
0.233 |
|
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 |
0.231 |
|
2022 |
Opoku-Nsiah KA, de la Pena AH, Williams SK, Chopra N, Sali A, Lander GC, Gestwicki JE. The YΦ motif defines the structure-activity relationships of human 20S proteasome activators. Nature Communications. 13: 1226. PMID 35264557 DOI: 10.1038/s41467-022-28864-x |
0.229 |
|
2005 |
Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP. Correction: Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture Plos Biology. 3: e80. DOI: 10.1371/Journal.Pbio.0030080 |
0.229 |
|
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 |
0.227 |
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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 |
0.227 |
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2024 |
Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM. Structural basis of prostaglandin efflux by MRP4. Nature Structural & Molecular Biology. PMID 38216659 DOI: 10.1038/s41594-023-01176-4 |
0.225 |
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2022 |
Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, ... ... Sali A, et al. RCSB Protein Data Bank: Tools for visualizing and understanding biological macromolecules in 3D. Protein Science : a Publication of the Protein Society. e4482. PMID 36281733 DOI: 10.1002/pro.4482 |
0.224 |
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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 |
0.224 |
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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 |
0.221 |
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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 |
0.221 |
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2012 |
Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P. Research priorities. Shining light into black boxes. Science (New York, N.Y.). 336: 159-60. PMID 22499926 DOI: 10.1126/Science.1218263 |
0.219 |
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1997 |
Sheng Y, Krilis SA, Sali A. Site-directed Mutagenesis of Recombinant Human β2-Glycoprotein I Effect of Phospholipid Binding and Anticardiolipin Antibody Activity Annals of the New York Academy of Sciences. 815: 331-333. PMID 9186672 DOI: 10.1111/J.1749-6632.1997.Tb52077.X |
0.219 |
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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 |
0.218 |
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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 |
0.217 |
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2022 |
Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, et al. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules. 12. PMID 36291635 DOI: 10.3390/biom12101425 |
0.214 |
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2022 |
Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. Elife. 11. PMID 35485925 DOI: 10.7554/eLife.66975 |
0.214 |
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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 |
0.212 |
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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 |
0.21 |
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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 |
0.209 |
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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 |
0.208 |
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2023 |
Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. Implications of a multiscale structure of the yeast nuclear pore complex. Molecular Cell. 83: 3283-3302.e5. PMID 37738963 DOI: 10.1016/j.molcel.2023.08.025 |
0.204 |
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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 |
0.204 |
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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 |
0.202 |
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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 |
0.199 |
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2023 |
Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature. PMID 36599981 DOI: 10.1038/s41586-022-05528-w |
0.192 |
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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 |
0.188 |
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2005 |
Devos D, Alber F, Dokudovskaya S, Chait B, Rout M, Sali A. Structural characterisation of the Nuclear Pore Complex Gbm Annual Spring Meeting Mosbach 2005. 2005. DOI: 10.1240/sav_gbm_2005_m_000910 |
0.187 |
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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 |
0.185 |
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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 |
0.183 |
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2007 |
Sali A, Lima CD, Kostic M. Structural genomics. Structure (London, England : 1993). 15: 1341. PMID 17997955 DOI: 10.1016/j.str.2007.10.009 |
0.182 |
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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 |
0.182 |
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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 |
0.176 |
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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 |
0.171 |
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2023 |
Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, et al. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. Research Square. PMID 37790518 DOI: 10.21203/rs.3.rs-3263845/v1 |
0.167 |
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2023 |
Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, et al. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. Biorxiv : the Preprint Server For Biology. PMID 37609337 DOI: 10.1101/2023.08.08.552553 |
0.167 |
|
2023 |
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Biorxiv : the Preprint Server For Biology. PMID 37961561 DOI: 10.1101/2023.10.28.564055 |
0.161 |
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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 |
0.16 |
|
2022 |
Li A, Zhang S, Loconte V, Liu Y, Ekman A, Thompson GJ, Sali A, Stevens RC, White K, Singla J, Sun L. An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms. Plos One. 17: e0269887. PMID 36048824 DOI: 10.1371/journal.pone.0269887 |
0.153 |
|
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. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. Elife. 10. PMID 34874007 DOI: 10.7554/eLife.73027 |
0.152 |
|
2002 |
Bello V, Goding JW, Greengrass V, Sali A, Dubljevic V, Lenoir C, Trugnan G, Maurice M. Characterization of a di-leucine-based signal in the cytoplasmic tail of the nucleotide-pyrophosphatase NPP1 that mediates basolateral targeting but not endocytosis. Molecular Biology of the Cell. 12: 3004-15. PMID 11598187 DOI: 10.1091/MBC.12.10.3004 |
0.149 |
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2023 |
Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, et al. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. Biorxiv : the Preprint Server For Biology. PMID 37066338 DOI: 10.1101/2023.03.31.535055 |
0.135 |
|
2023 |
Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. Biorxiv : the Preprint Server For Biology. PMID 37503298 DOI: 10.1101/2023.07.14.549041 |
0.132 |
|
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 |
0.13 |
|
2022 |
Li A, Zhang X, Singla J, White K, Loconte V, Hu C, Zhang C, Li S, Li W, Francis JP, Wang C, Sali A, Sun L, He X, Stevens RC. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. Plos One. 17: e0265567. PMID 35324950 DOI: 10.1371/journal.pone.0265567 |
0.128 |
|
2022 |
Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali A, Condello C, DeGrado WF. Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35082148 DOI: 10.1073/pnas.2114486119 |
0.114 |
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2022 |
Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Le Gros M, White KL, Larabell CA. Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure (London, England : 1993). PMID 35148829 DOI: 10.1016/j.str.2022.01.006 |
0.11 |
|
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 |
0.103 |
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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 |
0.102 |
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2001 |
Logsdon J, Fickett J, Koonin E, Sali A, Stormo G, Borodovsky M. The third Georgia Tech-Emory International Conference on Bioinformatics - In silico biology: Bioinformatics after the human genome (November 15-18, 2001, Atlanta, Georgia, USA) Bioinformatics. 17: 859-861. |
0.096 |
|
2023 |
Li W, Li A, Yu B, Zhang X, Liu X, White K, Stevens R, Baumeister W, Sali A, Jasnin M, Sun L. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Research Square. PMID 37066286 DOI: 10.21203/rs.3.rs-2694866/v1 |
0.095 |
|
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 |
0.092 |
|
2024 |
Li W, Li A, Yu B, Zhang X, Liu X, White KL, Stevens RC, Baumeister W, Sali A, Jasnin M, Sun L. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Nature Communications. 15: 1311. PMID 38346988 DOI: 10.1038/s41467-024-45648-7 |
0.079 |
|
2023 |
Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Gros ML, White KL, Larabell CA. Soft X-ray Tomography for Mapping and Quantifying Intracellular Organelle Interactions. Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 29: 1181. PMID 37613466 DOI: 10.1093/micmic/ozad067.607 |
0.078 |
|
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 |
0.078 |
|
2017 |
Xu KZ, Anderson BA, Emeric EE, Sali AW, Stuphorn V, Yantis S, Courtney SM. Neural Basis of Cognitive Control over Movement Inhibition: Human fMRI and Primate Electrophysiology Evidence. Neuron. PMID 29224723 DOI: 10.1016/J.Neuron.2017.11.010 |
0.065 |
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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 |
0.055 |
|
2022 |
Guo A, Zhang J, He B, Li A, Sun T, Li W, Wang J, Tai R, Liu Y, Qian Z, Fan J, Sali A, Stevens RC, Jiang H. Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic beta cells. Proceedings of the National Academy of Sciences of the United States of America. 119: e2202695119. PMID 35921440 DOI: 10.1073/pnas.2202695119 |
0.047 |
|
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 |
0.037 |
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2001 |
Sali A. Target practice. Nature Structural Biology. 8: 482-4. PMID 11373610 DOI: 10.1038/88529 |
0.036 |
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