| Year |
Citation |
Score |
| 2024 |
Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, Vajda S. Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. Journal of Chemical Information and Modeling. PMID 38456842 DOI: 10.1021/acs.jcim.3c01969 |
0.376 |
|
| 2024 |
Bekar-Cesaretli AA, Khan O, Nguyen T, Kozakov D, Joseph-Mccarthy D, Vajda S. Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. Journal of Chemical Information and Modeling. 64: 960-973. PMID 38253327 DOI: 10.1021/acs.jcim.3c01761 |
0.436 |
|
| 2023 |
Kotelnikov S, Ashizawa R, Popov KI, Khan O, Ignatov M, Li SX, Hassan M, Coutsias EA, Poda G, Padhorny D, Tropsha A, Vajda S, Kozakov D. Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server. Proteins. PMID 37697630 DOI: 10.1002/prot.26587 |
0.359 |
|
| 2023 |
Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. Journal of the American Chemical Society. 145: 7123-7135. PMID 36961978 DOI: 10.1021/jacs.2c09387 |
0.372 |
|
| 2022 |
Wakefield AE, Bajusz D, Kozakov D, Keserű GM, Vajda S. Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. Journal of Chemical Information and Modeling. 62: 4937-4954. PMID 36195573 DOI: 10.1021/acs.jcim.2c00209 |
0.407 |
|
| 2022 |
Ma S, Sun Z, Jing Y, McGann M, Vajda S, Enyedy IJ. Use of Solvent Mapping for Characterizing the Binding Site and for Predicting the Inhibition of the Human Ether-á-Go-Go-Related K Channel. Chemical Research in Toxicology. 35: 1359-1369. PMID 35895844 DOI: 10.1021/acs.chemrestox.2c00036 |
0.301 |
|
| 2022 |
Egbert M, Jones G, Collins MR, Kozakov D, Vajda S. FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures. Journal of Molecular Biology. 434: 167587. PMID 35662465 DOI: 10.1016/j.jmb.2022.167587 |
0.408 |
|
| 2022 |
Jones G, Jindal A, Ghani U, Kotelnikov S, Egbert M, Hashemi N, Vajda S, Padhorny D, Kozakov D. Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap. Acta Crystallographica. Section D, Structural Biology. 78: 690-697. PMID 35647916 DOI: 10.1107/S2059798322002741 |
0.358 |
|
| 2022 |
Wakefield AE, Kozakov D, Vajda S. Mapping the binding sites of challenging drug targets. Current Opinion in Structural Biology. 75: 102396. PMID 35636004 DOI: 10.1016/j.sbi.2022.102396 |
0.388 |
|
| 2021 |
Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209 |
0.402 |
|
| 2021 |
Egbert M, Porter KA, Ghani U, Kotelnikov S, Nguyen T, Ashizawa R, Kozakov D, Vajda S. Conservation of binding properties in protein models. Computational and Structural Biotechnology Journal. 19: 2549-2566. PMID 34025942 DOI: 10.1016/j.csbj.2021.04.048 |
0.423 |
|
| 2020 |
Wakefield AE, Yueh C, Beglov D, Castilho MS, Kozakov D, Keserű GM, Whitty A, Vajda S. Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. Journal of Chemical Information and Modeling. PMID 33291870 DOI: 10.1021/acs.jcim.0c00877 |
0.363 |
|
| 2020 |
Desta IT, Porter KA, Xia B, Kozakov D, Vajda S. Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure (London, England : 1993). PMID 32649857 DOI: 10.1016/J.Str.2020.06.006 |
0.698 |
|
| 2020 |
Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Furman OS, Vajda S, Kozakov D. ClusPro in rounds 38-45 of CAPRI: Toward combining template-based methods with free docking. Proteins. PMID 32142178 DOI: 10.1002/Prot.25887 |
0.698 |
|
| 2019 |
Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, Dill K, Vajda S, Kozakov D, Schueler-Furman O. Modeling beta sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI Rounds 38-45. Proteins. PMID 31891416 DOI: 10.1002/Prot.25871 |
0.613 |
|
| 2019 |
Alekseenko A, Kotelnikov S, Ignatov M, Egbert M, Kholodov Y, Vajda S, Kozakov D. ClusPro LigTBM: Automated Template-Based Small Molecule Docking. Journal of Molecular Biology. PMID 31863748 DOI: 10.1016/J.Jmb.2019.12.011 |
0.705 |
|
| 2019 |
Zhong M, Lynch AJ, Muellers SN, Jehle S, Luo L, Hall DR, Iwase R, Carolan JP, Egbert M, Wakefield A, Streu K, Harvey CM, Ortet PC, Kozakov D, Vajda S, et al. Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-associated Protein 1 (KEAP1) and Nuclear Factor, Erythroid 2 Like 2 (Nrf2). Biochemistry. PMID 31851823 DOI: 10.1021/Acs.Biochem.9B00943 |
0.777 |
|
| 2019 |
Sun Z, Wakefield AE, Kolossvary I, Beglov D, Vajda S. Structure-Based Analysis of Cryptic-Site Opening. Structure (London, England : 1993). PMID 31810712 DOI: 10.1016/J.Str.2019.11.007 |
0.486 |
|
| 2019 |
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Vajda S, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838 |
0.673 |
|
| 2019 |
Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D, Kotelnikov S, Sun Z, Alekseenko A, Anishchenko I, Cong Q, Ovchinnikov S, Baker D, Vajda S, Kozakov D. Template-Based Modeling by ClusPro in CASP13 and the Potential for Using Co-evolutionary Information in Docking. Proteins. PMID 31444975 DOI: 10.1002/Prot.25808 |
0.643 |
|
| 2019 |
Vajda S, Emili A. Mapping global protein contacts. Science (New York, N.Y.). 365: 120-121. PMID 31296755 DOI: 10.1126/Science.Aay1440 |
0.345 |
|
| 2019 |
Yueh C, Rettenmaier J, Xia B, Hall DR, Alekseenko A, Porter KA, Barkovich K, Keseru G, Whitty A, Wells JA, Vajda S, Kozakov D. Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. Journal of Medicinal Chemistry. PMID 31274316 DOI: 10.1021/Acs.Jmedchem.9B00089 |
0.704 |
|
| 2019 |
Egbert M, Whitty A, Keseru GM, Vajda S. Why some targets benefit from beyond rule of five drugs. Journal of Medicinal Chemistry. PMID 31188592 DOI: 10.1021/Acs.Jmedchem.8B01732 |
0.378 |
|
| 2019 |
Froes TQ, Baldini RL, Vajda S, Castilho MS. Structure-based druggability assessment of anti-virulence targets from Pseudomonas aeruginosa. Current Protein & Peptide Science. PMID 31038064 DOI: 10.2174/1389203720666190417120758 |
0.378 |
|
| 2019 |
Wakefield AE, Mason JS, Vajda S, Keserű GM. Analysis of tractable allosteric sites in G protein-coupled receptors. Scientific Reports. 9: 6180. PMID 30992500 DOI: 10.1038/S41598-019-42618-8 |
0.454 |
|
| 2019 |
Porter KA, Desta I, Kozakov D, Vajda S. What method to use for protein-protein docking? Current Opinion in Structural Biology. 55: 1-7. PMID 30711743 DOI: 10.1016/J.Sbi.2018.12.010 |
0.7 |
|
| 2019 |
Trilles R, Beglov D, Chen Q, He H, Wireman R, Reed A, Chennamadhavuni S, Panek JS, Brown LE, Vajda S, Porco JA, Kelley MR, Georgiadis MM. Discovery of macrocyclic inhibitors of Apurinic/apyrimidinic endonuclease 1. Journal of Medicinal Chemistry. PMID 30653918 DOI: 10.1021/Acs.Jmedchem.8B01529 |
0.341 |
|
| 2018 |
Vajda S, Beglov D, Wakefield AE, Egbert M, Whitty A. Cryptic binding sites on proteins: definition, detection, and druggability. Current Opinion in Chemical Biology. 44: 1-8. PMID 29800865 DOI: 10.1016/J.Cbpa.2018.05.003 |
0.465 |
|
| 2018 |
Zarbafian S, Moghadasi M, Roshandelpoor A, Nan F, Li K, Vakli P, Vajda S, Kozakov D, Paschalidis IC. Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes. Scientific Reports. 8: 5896. PMID 29650980 DOI: 10.1038/S41598-018-23982-3 |
0.695 |
|
| 2018 |
Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN, Kozakov D, Whitty A, Vajda S. Exploring the structural origins of cryptic sites on proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 29581267 DOI: 10.1073/Pnas.1711490115 |
0.759 |
|
| 2017 |
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. Nature Protocols. 12: 255-278. PMID 28079879 DOI: 10.1038/Nprot.2016.169 |
0.762 |
|
| 2016 |
Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New Additions to the ClusPro Server Motivated by CAPRI. Proteins. PMID 27936493 DOI: 10.1002/Prot.25219 |
0.737 |
|
| 2016 |
Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S. ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking. Journal of Molecular Biology. PMID 27771482 DOI: 10.1016/J.Jmb.2016.10.019 |
0.754 |
|
| 2016 |
Padhorny D, Kazennov A, Zerbe BS, Porter KA, Xia B, Mottarella SE, Kholodov Y, Ritchie DW, Vajda S, Kozakov D. Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. Proceedings of the National Academy of Sciences of the United States of America. PMID 27412858 DOI: 10.1073/Pnas.1603929113 |
0.82 |
|
| 2016 |
Xia B, Vajda S, Kozakov D. Accounting for pairwise distance restraints in FFT based protein-protein docking. Bioinformatics (Oxford, England). PMID 27357172 DOI: 10.1093/Bioinformatics/Btw306 |
0.691 |
|
| 2016 |
Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. Journal of Molecular Biology. PMID 27255863 DOI: 10.1016/J.Jmb.2016.05.024 |
0.363 |
|
| 2016 |
Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. PMID 27172383 DOI: 10.1002/Prot.25063 |
0.713 |
|
| 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, ... ... Vajda S, 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 |
0.743 |
|
| 2016 |
Whitty A, Zhong M, Viarengo L, Beglov D, Hall DR, Vajda S. Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs. Drug Discovery Today. PMID 26891978 DOI: 10.1016/J.Drudis.2016.02.005 |
0.496 |
|
| 2016 |
Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Ch Paschalidis I, Vajda S, Kozakov D. Focused grid-based resampling for protein docking and mapping. Journal of Computational Chemistry. PMID 26837000 DOI: 10.1002/Jcc.24273 |
0.732 |
|
| 2015 |
Lukose V, Luo L, Kozakov D, Vajda S, Allen KN, Imperiali B. Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identifies the Functional Catalytic Core. Biochemistry. PMID 26600273 DOI: 10.1021/Acs.Biochem.5B01086 |
0.613 |
|
| 2015 |
Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends in Pharmacological Sciences. 36: 724-36. PMID 26538314 DOI: 10.1016/J.Tips.2015.08.003 |
0.741 |
|
| 2015 |
Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis IC, Vakili P, Kozakov D. Energy minimization on manifolds for docking flexible molecules. Journal of Chemical Theory and Computation. 11: 1063-1076. PMID 26478722 DOI: 10.1021/Ct500155T |
0.679 |
|
| 2015 |
Vajda S, Whitty A, Kozakov D. Fragments and hot spots in drug discovery. Oncotarget. 6: 18740-1. PMID 26300051 DOI: 10.18632/Oncotarget.4968 |
0.721 |
|
| 2015 |
Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S. New Frontiers in Druggability. Journal of Medicinal Chemistry. PMID 26230724 DOI: 10.1021/Acs.Jmedchem.5B00586 |
0.811 |
|
| 2015 |
Kozakov D, Vakili P, Paschalidis ICh, Vajda S. 46 Encounter complexes and dimensionality reduction in protein-protein association. Journal of Biomolecular Structure & Dynamics. 33: 32. PMID 26103257 DOI: 10.1080/07391102.2015.1032595 |
0.612 |
|
| 2015 |
Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis ICh, Vajda S, Kozakov D. Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. Journal of Computational Chemistry. 36: 1568-72. PMID 26095982 DOI: 10.1002/Jcc.23952 |
0.69 |
|
| 2015 |
Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proceedings of the National Academy of Sciences of the United States of America. 112: E2585-94. PMID 25918377 DOI: 10.1073/Pnas.1501567112 |
0.754 |
|
| 2015 |
Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE, Luo L, Xia B, Beglov D, Vajda S. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nature Protocols. 10: 733-55. PMID 25855957 DOI: 10.1038/Nprot.2015.043 |
0.79 |
|
| 2015 |
Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S, Paschalidis ICh, Kozakov D. The impact of side-chain packing on protein docking refinement. Journal of Chemical Information and Modeling. 55: 872-81. PMID 25714358 DOI: 10.1021/Ci500380A |
0.672 |
|
| 2014 |
Nan F, Moghadasi M, Vakili P, Vajda S, Kozakov D, Ch Paschalidis I. A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. Proceedings of the ... Ieee Conference On Decision & Control / Ieee Control Systems Society. Ieee Conference On Decision & Control. 2014: 4623-4628. PMID 25914440 DOI: 10.1109/CDC.2014.7040111 |
0.635 |
|
| 2014 |
Vakili P, Mirzaei H, Zarbafian S, Paschalidis IC, Kozakov D, Vajda S. Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach. Proceedings of the ... Ieee Conference On Decision & Control / Ieee Control Systems Society. Ieee Conference On Decision & Control. 2014: 5825-5830. PMID 25774073 DOI: 10.1109/CDC.2014.7040301 |
0.547 |
|
| 2014 |
Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P, Vajda S, Bajaj C, Kozakov D. Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations. Journal of Chemical Theory and Computation. 10: 4449-4454. PMID 25328494 DOI: 10.1021/Ct400474W |
0.614 |
|
| 2014 |
Bohnuud T, Kozakov D, Vajda S. Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces. Plos Computational Biology. 10: e1003872. PMID 25275445 DOI: 10.1371/Journal.Pcbi.1003872 |
0.742 |
|
| 2014 |
Parks AJ, Pollastri MP, Hahn ME, Stanford EA, Novikov O, Franks DG, Haigh SE, Narasimhan S, Ashton TD, Hopper TG, Kozakov D, Beglov D, Vajda S, Schlezinger JJ, Sherr DH. In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo. Molecular Pharmacology. 86: 593-608. PMID 25159092 DOI: 10.1124/Mol.114.093369 |
0.609 |
|
| 2014 |
Pillai HK, Fang M, Beglov D, Kozakov D, Vajda S, Stapleton HM, Webster TF, Schlezinger JJ. Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro. Environmental Health Perspectives. 122: 1225-32. PMID 25062436 DOI: 10.1289/Ehp.1408111 |
0.613 |
|
| 2014 |
Villar EA, Beglov D, Chennamadhavuni S, Porco JA, Kozakov D, Vajda S, Whitty A. How proteins bind macrocycles. Nature Chemical Biology. 10: 723-31. PMID 25038790 DOI: 10.1038/Nchembio.1584 |
0.707 |
|
| 2014 |
Mottarella SE, Beglov D, Beglova N, Nugent MA, Kozakov D, Vajda S. Docking server for the identification of heparin binding sites on proteins. Journal of Chemical Information and Modeling. 54: 2068-78. PMID 24974889 DOI: 10.1021/Ci500115J |
0.735 |
|
| 2014 |
Bogorad AM, Xia B, Sandor DG, Mamonov AB, Cafarella TR, Jehle S, Vajda S, Kozakov D, Marintchev A. Insights into the architecture of the eIF2Bα/β/δ regulatory subcomplex. Biochemistry. 53: 3432-45. PMID 24811713 DOI: 10.1021/Bi500346U |
0.612 |
|
| 2014 |
Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S. Encounter complexes and dimensionality reduction in protein-protein association. Elife. 3: e01370. PMID 24714491 DOI: 10.7554/Elife.01370 |
0.752 |
|
| 2014 |
Shin U, Williams DE, Kozakov D, Hall DR, Beglov D, Vajda S, Andersen RJ, Pelletier J. Stimulators of translation identified during a small molecule screening campaign. Analytical Biochemistry. 447: 6-14. PMID 24513115 DOI: 10.1016/J.Ab.2013.10.026 |
0.688 |
|
| 2014 |
Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Vajda S, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439 |
0.65 |
|
| 2014 |
Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis IC, Clore GM, Vajda S. Author response: Encounter complexes and dimensionality reduction in protein–protein association Elife. DOI: 10.7554/Elife.01370.021 |
0.461 |
|
| 2013 |
Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC. A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking(*) Proceedings of the ... Ieee Conference On Decision & Control / Ieee Control Systems Society. Ieee Conference On Decision & Control. 739-744. PMID 24844567 DOI: 10.1109/CDC.2013.6759970 |
0.635 |
|
| 2013 |
Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P. Flexible Refinement of Protein-Ligand Docking on Manifolds. Proceedings of the ... Ieee Conference On Decision & Control / Ieee Control Systems Society. Ieee Conference On Decision & Control. 1392-1397. PMID 24830567 DOI: 10.1109/CDC.2013.6760077 |
0.628 |
|
| 2013 |
Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S. How good is automated protein docking? Proteins. 81: 2159-66. PMID 23996272 DOI: 10.1002/Prot.24403 |
0.73 |
|
| 2013 |
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Vajda S, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356 |
0.722 |
|
| 2013 |
Vajda S, Hall DR, Kozakov D. Sampling and scoring: a marriage made in heaven. Proteins. 81: 1874-84. PMID 23775627 DOI: 10.1002/Prot.24343 |
0.749 |
|
| 2013 |
Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA, Beglov D, Sazinsky SL, Georgiadis RM, Vajda S, Kozakov D, Whitty A. Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface. Journal of the American Chemical Society. 135: 6242-56. PMID 23506214 DOI: 10.1021/Ja400914Z |
0.831 |
|
| 2013 |
Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D. FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics (Oxford, England). 29: 1218-9. PMID 23476022 DOI: 10.1093/Bioinformatics/Btt102 |
0.744 |
|
| 2013 |
Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC. A new distributed algorithm for side-chain repacking in protein-protein association F1000research. 4. DOI: 10.7490/F1000Research.1093112.1 |
0.338 |
|
| 2013 |
Bohnuud T, Beglov D, Ngan C, Zerbe B, Hall D, Brenke R, Vajda S, Frank-Kamenetskii M, Kozakov D. 89 Computational mapping reveals effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde Journal of Biomolecular Structure and Dynamics. 31: 57-57. DOI: 10.1080/07391102.2013.786523 |
0.767 |
|
| 2012 |
Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P. A New Approach to Rigid Body Minimization with Application to Molecular Docking. Proceedings of the ... Ieee Conference On Decision & Control / Ieee Control Systems Society. Ieee Conference On Decision & Control. 2983-2988. PMID 24763338 DOI: 10.1109/CDC.2012.6426267 |
0.617 |
|
| 2012 |
Moghadasi M, Kozakov D, Mamonov AB, Vakili P, Vajda S, Paschalidis IC. A Message Passing Approach to Side Chain Positioning with Applications in Protein Docking Refinement. Proceedings of the ... Ieee Conference On Decision & Control / Ieee Control Systems Society. Ieee Conference On Decision & Control. 2310-2315. PMID 23515575 DOI: 10.1109/CDC.2012.6426600 |
0.615 |
|
| 2012 |
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D. Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. 8: 4374-4380. PMID 23382659 DOI: 10.1021/Ct300272J |
0.648 |
|
| 2012 |
Brenke R, Hall DR, Chuang GY, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics (Oxford, England). 28: 2608-14. PMID 23053206 DOI: 10.1093/Bioinformatics/Bts493 |
0.797 |
|
| 2012 |
Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo JL, Dash R, Sarkar D, Hall D, Kozakov D, Vajda S, Fisher PB, Shah K. A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy. Plos One. 7: e40234. PMID 22808125 DOI: 10.1371/Journal.Pone.0040234 |
0.662 |
|
| 2012 |
Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D. Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. Journal of Chemical Information and Modeling. 52: 2236-44. PMID 22770357 DOI: 10.1021/Ci300175U |
0.846 |
|
| 2012 |
Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D. Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Research. 40: 7644-52. PMID 22705795 DOI: 10.1093/Nar/Gks519 |
0.766 |
|
| 2012 |
Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S. FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Research. 40: W271-5. PMID 22589414 DOI: 10.1093/Nar/Gks441 |
0.83 |
|
| 2012 |
Hall DR, Kozakov D, Vajda S. Analysis of protein binding sites by computational solvent mapping. Methods in Molecular Biology (Clifton, N.J.). 819: 13-27. PMID 22183527 DOI: 10.1007/978-1-61779-465-0_2 |
0.788 |
|
| 2012 |
Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. Journal of Chemical Information and Modeling. 52: 199-209. PMID 22145575 DOI: 10.1021/Ci200468P |
0.82 |
|
| 2012 |
Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, Vajda S. FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics (Oxford, England). 28: 286-7. PMID 22113084 DOI: 10.1093/Bioinformatics/Btr651 |
0.824 |
|
| 2012 |
Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL, Kozakov D, Vajda S. Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins. 80: 591-601. PMID 22105850 DOI: 10.1002/Prot.23222 |
0.823 |
|
| 2011 |
Hall DH, Grove LE, Yueh C, Ngan CH, Kozakov D, Vajda S. Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme. Journal of the American Chemical Society. 133: 20668-71. PMID 22092261 DOI: 10.1021/Ja207914Y |
0.843 |
|
| 2011 |
Buhrman G, O'Connor C, Zerbe B, Kearney BM, Napoleon R, Kovrigina EA, Vajda S, Kozakov D, Kovrigin EL, Mattos C. Analysis of binding site hot spots on the surface of Ras GTPase. Journal of Molecular Biology. 413: 773-89. PMID 21945529 DOI: 10.1016/J.Jmb.2011.09.011 |
0.775 |
|
| 2011 |
Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S. Structural conservation of druggable hot spots in protein-protein interfaces. Proceedings of the National Academy of Sciences of the United States of America. 108: 13528-33. PMID 21808046 DOI: 10.1073/Pnas.1101835108 |
0.848 |
|
| 2011 |
Callard GV, Tarrant AM, Novillo A, Yacci P, Ciaccia L, Vajda S, Chuang GY, Kozakov D, Greytak SR, Sawyer S, Hoover C, Cotter KA. Evolutionary origins of the estrogen signaling system: insights from amphioxus. The Journal of Steroid Biochemistry and Molecular Biology. 127: 176-88. PMID 21514383 DOI: 10.1016/J.Jsbmb.2011.03.022 |
0.692 |
|
| 2011 |
Cencic R, Desforges M, Hall DR, Kozakov D, Du Y, Min J, Dingledine R, Fu H, Vajda S, Talbot PJ, Pelletier J. Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication. Journal of Virology. 85: 6381-9. PMID 21507972 DOI: 10.1128/Jvi.00078-11 |
0.703 |
|
| 2011 |
Cencic R, Hall DR, Robert F, Du Y, Min J, Li L, Qui M, Lewis I, Kurtkaya S, Dingledine R, Fu H, Kozakov D, Vajda S, Pelletier J. Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F. Proceedings of the National Academy of Sciences of the United States of America. 108: 1046-51. PMID 21191102 DOI: 10.1073/Pnas.1011477108 |
0.699 |
|
| 2010 |
Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis ICh, Vajda S. Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins. 78: 3124-30. PMID 20818657 DOI: 10.1002/Prot.22835 |
0.829 |
|
| 2010 |
Chuang GY, Mehra-Chaudhary R, Ngan CH, Zerbe BS, Kozakov D, Vajda S, Beamer LJ. Domain motion and interdomain hot spots in a multidomain enzyme. Protein Science : a Publication of the Protein Society. 19: 1662-72. PMID 20589904 DOI: 10.1002/Pro.446 |
0.812 |
|
| 2010 |
Kozakov D, Chuang GY, Beglov D, Vajda S. Where does amantadine bind to the influenza virus M2 proton channel? Trends in Biochemical Sciences. 35: 471-5. PMID 20382026 DOI: 10.1016/J.Tibs.2010.03.006 |
0.738 |
|
| 2009 |
Chuang GY, Kozakov D, Brenke R, Beglov D, Guarnieri F, Vajda S. Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel. Biophysical Journal. 97: 2846-53. PMID 19917240 DOI: 10.1016/J.Bpj.2009.09.004 |
0.823 |
|
| 2009 |
Ngan CH, Beglov D, Rudnitskaya AN, Kozakov D, Waxman DJ, Vajda S. The structural basis of pregnane X receptor binding promiscuity. Biochemistry. 48: 11572-81. PMID 19856963 DOI: 10.1021/Bi901578N |
0.836 |
|
| 2009 |
Beglov D, Lee CJ, De Biasio A, Kozakov D, Brenke R, Vajda S, Beglova N. Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors. Proteins. 77: 940-9. PMID 19676115 DOI: 10.1002/Prot.22519 |
0.8 |
|
| 2009 |
Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JM, Orwig SD, Kozakov D, Brenke R, Chuang GY, Beglov D, Vajda S, Petsko GA, Ringe D. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. Journal of Computer-Aided Molecular Design. 23: 491-500. PMID 19521672 DOI: 10.1007/S10822-009-9283-2 |
0.836 |
|
| 2009 |
Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Current Opinion in Structural Biology. 19: 164-70. PMID 19327983 DOI: 10.1016/J.Sbi.2009.02.008 |
0.685 |
|
| 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, ... ... Vajda S, 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 |
0.306 |
|
| 2009 |
Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics (Oxford, England). 25: 621-7. PMID 19176554 DOI: 10.1093/Bioinformatics/Btp036 |
0.829 |
|
| 2008 |
Shen Y, Paschalidis ICh, Vakili P, Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. Plos Computational Biology. 4: e1000191. PMID 18846200 DOI: 10.1371/Journal.Pcbi.1000191 |
0.428 |
|
| 2008 |
Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S. DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophysical Journal. 95: 4217-27. PMID 18676649 DOI: 10.1529/Biophysj.108.135814 |
0.804 |
|
| 2008 |
Ritchie DW, Kozakov D, Vajda S. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics (Oxford, England). 24: 1865-73. PMID 18591193 DOI: 10.1093/Bioinformatics/Btn334 |
0.67 |
|
| 2008 |
Kozakov D, Schueler-Furman O, Vajda S. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins. 72: 993-1004. PMID 18300245 DOI: 10.1002/Prot.21997 |
0.672 |
|
| 2008 |
Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S. Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chemical Biology & Drug Design. 71: 106-16. PMID 18205727 DOI: 10.1111/J.1747-0285.2007.00614.X |
0.802 |
|
| 2008 |
Kaya T, Kozakov D, Vajda S. Clustering versus scoring for the identification of near-native poses in protein-ligand docking Proceedings of the 2008 International Conference On Bioinformatics and Computational Biology, Biocomp 2008. 1028-1032. |
0.654 |
|
| 2007 |
Paschalidis IC, Shen Y, Vakili P, Vajda S. SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. Ieee Transactions On Automatic Control. 52: 664-676. PMID 19759849 DOI: 10.1109/Tac.2007.894518 |
0.424 |
|
| 2007 |
Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S. ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins. 69: 781-5. PMID 17876812 DOI: 10.1002/Prot.21795 |
0.823 |
|
| 2007 |
Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S. Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI. Proteins. 69: 734-42. PMID 17853451 DOI: 10.1002/Prot.21754 |
0.826 |
|
| 2007 |
Silberstein M, Damborsky J, Vajda S. Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. 46: 9239-49. PMID 17645312 DOI: 10.1021/Bi700336Y |
0.643 |
|
| 2007 |
Landon MR, Lancia DR, Yu J, Thiel SC, Vajda S. Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. Journal of Medicinal Chemistry. 50: 1231-40. PMID 17305325 DOI: 10.1021/Jm061134B |
0.459 |
|
| 2007 |
Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ. Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs. Biochemistry. 46: 2640-54. PMID 17300179 DOI: 10.1021/Bi062320M |
0.787 |
|
| 2006 |
Paschalidis ICh, Shen Y, Vakili P, Vajda S. Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 1: 5330-3. PMID 17946298 DOI: 10.1109/IEMBS.2006.260790 |
0.328 |
|
| 2006 |
Silberstein M, Landon MR, Wang YE, Perl A, Vajda S. Computational methods for functional site identification suggest a substrate access channel in transaldolase. Genome Informatics. International Conference On Genome Informatics. 17: 13-22. PMID 17503352 DOI: 10.11234/Gi1990.17.13 |
0.657 |
|
| 2006 |
Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins. 65: 392-406. PMID 16933295 DOI: 10.1002/Prot.21117 |
0.825 |
|
| 2006 |
Kaya T, Mohr SC, Waxman DJ, Vajda S. Computational screening of phthalate monoesters for binding to PPARgamma. Chemical Research in Toxicology. 19: 999-1009. PMID 16918238 DOI: 10.1021/Tx050301S |
0.442 |
|
| 2006 |
Clodfelter KH, Waxman DJ, Vajda S. Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450. Biochemistry. 45: 9393-407. PMID 16878974 DOI: 10.1021/Bi060343V |
0.457 |
|
| 2006 |
Vajda S, Guarnieri F. Characterization of protein-ligand interaction sites using experimental and computational methods. Current Opinion in Drug Discovery & Development. 9: 354-62. PMID 16729732 |
0.398 |
|
| 2006 |
Landon MR, Lancia DR, Clodfelter KH, Vajda S. Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns. Journal of Molecular Graphics & Modelling. 24: 426-33. PMID 16221553 DOI: 10.1016/J.Jmgm.2005.08.004 |
0.372 |
|
| 2005 |
Comeau SR, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins. 60: 239-44. PMID 15981265 DOI: 10.1002/Prot.20564 |
0.821 |
|
| 2005 |
Vajda S. Classification of protein complexes based on docking difficulty. Proteins. 60: 176-80. PMID 15981248 DOI: 10.1002/Prot.20554 |
0.468 |
|
| 2005 |
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophysical Journal. 89: 867-75. PMID 15908573 DOI: 10.1529/Biophysj.104.058768 |
0.666 |
|
| 2005 |
Sheu SH, Kaya T, Waxman DJ, Vajda S. Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping. Biochemistry. 44: 1193-209. PMID 15667213 DOI: 10.1021/Bi048032C |
0.469 |
|
| 2005 |
Sheu SH, Lancia DR, Clodfelter KH, Landon MR, Vajda S. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Research. 33: D206-11. PMID 15608178 DOI: 10.1093/Nar/Gki091 |
0.391 |
|
| 2004 |
Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 101: 11287-92. PMID 15269345 DOI: 10.1073/Pnas.0401942101 |
0.771 |
|
| 2004 |
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research. 32: W96-9. PMID 15215358 DOI: 10.1093/Nar/Gkh354 |
0.815 |
|
| 2004 |
Prasad JC, Vajda S, Camacho CJ. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research. 32: W50-4. PMID 15215349 DOI: 10.1093/Nar/Gkh456 |
0.812 |
|
| 2004 |
Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends in Biotechnology. 22: 110-6. PMID 15036860 DOI: 10.1016/J.Tibtech.2004.01.006 |
0.459 |
|
| 2004 |
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics (Oxford, England). 20: 45-50. PMID 14693807 DOI: 10.1093/Bioinformatics/Btg371 |
0.823 |
|
| 2003 |
Murphy J, Gatchell DW, Prasad JC, Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins. 53: 840-54. PMID 14635126 DOI: 10.1002/Prot.10473 |
0.819 |
|
| 2003 |
Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter K, Vajda S. Identification of substrate binding sites in enzymes by computational solvent mapping. Journal of Molecular Biology. 332: 1095-113. PMID 14499612 DOI: 10.1016/J.Jmb.2003.08.019 |
0.811 |
|
| 2003 |
Kortvelyesi T, Silberstein M, Dennis S, Vajda S. Improved mapping of protein binding sites. Journal of Computer-Aided Molecular Design. 17: 173-86. PMID 13677484 DOI: 10.1023/A:1025369923311 |
0.826 |
|
| 2003 |
Prasad JC, Comeau SR, Vajda S, Camacho CJ. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics (Oxford, England). 19: 1682-91. PMID 12967965 DOI: 10.1093/Bioinformatics/Btg211 |
0.792 |
|
| 2003 |
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 52: 2-9. PMID 12784359 DOI: 10.1002/Prot.10381 |
0.468 |
|
| 2003 |
Kortvelyesi T, Dennis S, Silberstein M, Brown L, Vajda S. Algorithms for computational solvent mapping of proteins. Proteins. 51: 340-51. PMID 12696046 DOI: 10.1002/Prot.10287 |
0.804 |
|
| 2003 |
Prasad JC, Silberstein M, Camacho CJ, Vajda S. Homology modeling of proteins using multiple models and consensus sequence alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2812: 389-401. |
0.786 |
|
| 2002 |
Vajda S, Vakser IA, Sternberg MJ, Janin J. Modeling of protein interactions in genomes. Proteins. 47: 444-6. PMID 12001222 DOI: 10.1002/Prot.10112 |
0.325 |
|
| 2002 |
Dennis S, Vajda S. Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. Journal of Computational Chemistry. 23: 319-34. PMID 11908495 DOI: 10.1002/Jcc.10026 |
0.739 |
|
| 2002 |
Dennis S, Kortvelyesi T, Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proceedings of the National Academy of Sciences of the United States of America. 99: 4290-5. PMID 11904374 DOI: 10.1073/Pnas.062398499 |
0.771 |
|
| 2002 |
Camacho CJ, Vajda S. Protein-protein association kinetics and protein docking. Current Opinion in Structural Biology. 12: 36-40. PMID 11839487 DOI: 10.1016/S0959-440X(02)00286-5 |
0.479 |
|
| 2001 |
Reznik GO, Vajda S, Cantor CR, Sano T. A streptavidin mutant useful for directed immobilization on solid surfaces. Bioconjugate Chemistry. 12: 1000-4. PMID 11716692 DOI: 10.1021/Bc015507T |
0.334 |
|
| 2001 |
Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proceedings of the National Academy of Sciences of the United States of America. 98: 10636-41. PMID 11517309 DOI: 10.1073/Pnas.181147798 |
0.484 |
|
| 2001 |
Kimura SR, Brower RC, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition Biophysical Journal. 80: 635-642. PMID 11159432 DOI: 10.1016/S0006-3495(01)76044-4 |
0.434 |
|
| 2000 |
Gatchell DW, Dennis S, Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins. 41: 518-34. PMID 11056039 DOI: 10.1002/1097-0134(20001201)41:4<518::Aid-Prot90>3.0.Co;2-6 |
0.803 |
|
| 2000 |
Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins. 40: 525-37. PMID 10861944 DOI: 10.1002/1097-0134(20000815)40:3<525::Aid-Prot190>3.0.Co;2-F |
0.809 |
|
| 2000 |
Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophysical Journal. 78: 1094-105. PMID 10692300 DOI: 10.1016/S0006-3495(00)76668-9 |
0.424 |
|
| 2000 |
Dennis S, Camacho CJ, Vajda S. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins. 38: 176-88. PMID 10656264 DOI: 10.1002/(Sici)1097-0134(20000201)38:2<176::Aid-Prot6>3.0.Co;2-O |
0.734 |
|
| 1999 |
Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophysical Journal. 76: 1166-78. PMID 10049302 DOI: 10.1016/S0006-3495(99)77281-4 |
0.453 |
|
| 1998 |
Janardhan A, Vajda S. Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms Protein Science. 7: 1772-1780. PMID 10082374 DOI: 10.1002/Pro.5560070812 |
0.41 |
|
| 1998 |
Reznik GO, Vajda S, Sano T, Cantor CR. A streptavidin mutant with altered ligand-binding specificity. Proceedings of the National Academy of Sciences of the United States of America. 95: 13525-30. PMID 9811833 DOI: 10.1073/Pnas.95.23.13525 |
0.381 |
|
| 1998 |
Sano T, Vajda S, Cantor CR. Genetic engineering of streptavidin, a versatile affinity tag. Journal of Chromatography. B, Biomedical Sciences and Applications. 715: 85-91. PMID 9792500 DOI: 10.1016/S0378-4347(98)00316-8 |
0.367 |
|
| 1998 |
Zhang C, Kimura SR, Weng Z, Vajda S, Brower RC, Delisi C. The waters of life Journal of the Franklin Institute. 335: 213-240. DOI: 10.1016/S0016-0032(97)00020-3 |
0.364 |
|
| 1997 |
Weng Z, Delisi C, Vajda S. Empirical free energy calculation: Comparison to calorimetric data Protein Science. 6: 1976-1984. PMID 9300497 DOI: 10.1002/Pro.5560060918 |
0.4 |
|
| 1997 |
Sano T, Vajda S, Smith CL, Cantor CR. Engineering subunit association of multisubunit proteins: a dimeric streptavidin. Proceedings of the National Academy of Sciences of the United States of America. 94: 6153-8. PMID 9177186 DOI: 10.1073/Pnas.94.12.6153 |
0.389 |
|
| 1997 |
Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding Current Opinion in Structural Biology. 7: 222-228. PMID 9094333 DOI: 10.1016/S0959-440X(97)80029-2 |
0.441 |
|
| 1996 |
Reznik GO, Vajda S, Smith CL, Cantor CR, Sano T. Streptavidins with intersubunit crosslinks have enhanced stability Nature Biotechnology. 14: 1007-1011. PMID 9631041 DOI: 10.1038/Nbt0896-1007 |
0.326 |
|
| 1996 |
Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions Protein Science. 5: 614-626. PMID 8845751 DOI: 10.1002/Pro.5560050406 |
0.427 |
|
| 1996 |
Sezerman U, Vajda S, Delisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides Protein Science. 5: 1272-1281. PMID 8819160 DOI: 10.1002/Pro.5560050706 |
0.394 |
|
| 1996 |
King BL, Vajda S, DeLisi C. Empirical free energy as a target function in docking and design: Application to HIV-1 protease inhibitors Febs Letters. 384: 87-91. PMID 8797810 DOI: 10.1016/0014-5793(96)00276-1 |
0.449 |
|
| 1996 |
Gulukota K, Vajda S, Delisi C. Peptide docking using dynamic programming Journal of Computational Chemistry. 17: 418-428. DOI: 10.1002/(Sici)1096-987X(199603)17:4<418::Aid-Jcc4>3.0.Co;2-X |
0.335 |
|
| 1995 |
Vajda S, Weng Z, Delisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments Protein Engineering, Design and Selection. 8: 1081-1092. PMID 8819974 DOI: 10.1093/Protein/8.11.1081 |
0.378 |
|
| 1995 |
Rosenfeld R, Vajda S, DeLisi C. Flexible docking and design Annual Review of Biophysics and Biomolecular Structure. 24: 677-700. PMID 7663131 DOI: 10.1146/Annurev.Bb.24.060195.003333 |
0.407 |
|
| 1995 |
Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Flexible docking of peptides to class I major-histocompatibility-complex receptors Genetic Analysis: Biomolecular Engineering. 12: 1-21. PMID 7648466 DOI: 10.1016/1050-3862(95)00107-7 |
0.315 |
|
| 1994 |
Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor - Ligand binding free energies Biochemistry. 33: 13977-13988. PMID 7947806 DOI: 10.1021/Bi00251A004 |
0.415 |
|
| 1994 |
Buturovic LJ, Smith TF, Vajda S. Finite-state and reduced-parameter representations of protein backbone conformations Journal of Computational Chemistry. 15: 300-312. DOI: 10.1002/Jcc.540150305 |
0.385 |
|
| 1993 |
Rao S, Zhu QL, Vajda S, Smith T. The local information content of the protein structural database Febs Letters. 322: 143-146. PMID 8482381 DOI: 10.1016/0014-5793(93)81555-E |
0.397 |
|
| 1993 |
Vajda S, Jafri MS, Sezerman OU, DeLisi C. Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization. Biopolymers. 33: 173-92. PMID 8427934 DOI: 10.1002/Bip.360330117 |
0.383 |
|
| 1993 |
Vajda S. Conformational filtering in polypeptides and proteins Journal of Molecular Biology. 229: 125-145. PMID 8421296 DOI: 10.1006/Jmbi.1993.1013 |
0.392 |
|
| 1993 |
Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Determining protein loop conformation using scaling-relaxation techniques Protein Science. 2: 1242-1248. PMID 8401209 DOI: 10.1002/Pro.5560020806 |
0.371 |
|
| 1993 |
Figge J, Breese K, Vajda S, Zhu QL, Eisele L, Andersen TT, MacColl R, Friedrich T, Smith TF. The binding domain structure of retinoblastoma-binding proteins Protein Science. 2: 155-164. PMID 8382993 DOI: 10.1002/Pro.5560020204 |
0.445 |
|
| 1993 |
Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors Journal of Molecular Biology. 234: 515-521. PMID 8254656 DOI: 10.1006/Jmbi.1993.1607 |
0.339 |
|
| 1993 |
Sezerman U, Vajda S, Cornette J, DeLisi C. Toward computational determination of peptide-receptor structure Protein Science. 2: 1827-1843. PMID 7505681 DOI: 10.1002/Pro.5560021105 |
0.316 |
|
| 1993 |
Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Loop closure via bond scaling and relaxation Journal of Computational Chemistry. 14: 556-565. DOI: 10.1002/Jcc.540140508 |
0.36 |
|
| 1991 |
Eisenfeld J, Vajda S, Sugar I, DeLisi C. Constrained optimization and protein structure determination American Journal of Physiology - Cell Physiology. 261. PMID 1872378 DOI: 10.1152/Ajpcell.1991.261.2.C376 |
0.402 |
|
| 1990 |
Vajda S, Delisi C. Determining minimum energy conformations of polypeptides by dynamic programming Biopolymers. 29: 1755-1772. PMID 2207285 DOI: 10.1002/Bip.360291408 |
0.37 |
|
| 1990 |
Chappell MJ, Godfrey KR, Vajda S. Global identifiability of the parameters of nonlinear systems with specified inputs: A comparison of methods Mathematical Biosciences. 102: 41-73. PMID 2134490 DOI: 10.1016/0025-5564(90)90055-4 |
0.301 |
|
| 1988 |
Vajda S, Godfrey KR, Valko P. Numerical deconvolution using system identification methods Journal of Pharmacokinetics and Biopharmaceutics. 16: 85-107. PMID 3373420 DOI: 10.1007/Bf01061863 |
0.302 |
|
| 1984 |
Valko P, Vajda S. An extended ode solver for sensitivity calculations Computers and Chemistry. 8: 255-271. DOI: 10.1016/0097-8485(84)85017-2 |
0.311 |
|
| 1984 |
Vajda S. Analysis of unique structural identifiability via submodels Mathematical Biosciences. 71: 125-146. DOI: 10.1016/0025-5564(84)90023-3 |
0.345 |
|
| 1984 |
Vajda S. Structural equivalence and exhaustive compartmental modeling Mathematical Biosciences. 69: 57-75. DOI: 10.1016/0025-5564(84)90014-2 |
0.336 |
|
| 1981 |
Vajda S. Structural equivalence of linear systems and compartmental models Mathematical Biosciences. 55: 39-64. DOI: 10.1016/0025-5564(81)90012-2 |
0.319 |
|
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