Dmytro Kozakov, Ph.D. - Publications

Affiliations: 
2007 Boston University, Boston, MA, United States 
Area:
Biomedical Engineering

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

Year Citation  Score
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  1
2020 Alekseenko A, Ignatov M, Jones G, Sabitova M, Kozakov D. Protein-Protein and Protein-Peptide Docking with ClusPro Server. Methods in Molecular Biology (Clifton, N.J.). 2165: 157-174. PMID 32621224 DOI: 10.1007/978-1-0716-0708-4_9  0.6
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  1
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  1
2019 Kotelnikov S, Alekseenko A, Liu C, Ignatov M, Padhorny D, Brini E, Lukin M, Coutsias E, Dill KA, Kozakov D. Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 31879831 DOI: 10.1007/S10822-019-00257-1  0.6
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  1
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  1
2019 Wang J, Alekseenko A, Kozakov D, Miao Y. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. Frontiers in Molecular Biosciences. 6: 112. PMID 31737642 DOI: 10.3389/Fmolb.2019.00112  0.6
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, ... ... Kozakov D, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  1
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  1
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  1
2019 Brini E, Kozakov D, Dill KA. Predicting protein dimer structures using MELD x MD. Journal of Chemical Theory and Computation. PMID 30908034 DOI: 10.1021/Acs.Jctc.8B01208  0.6
2019 Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, ... ... Kozakov D, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003  0.6
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  1
2018 Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D, Kotelnikov S, Kazennov A, Grebenkin I, Kholodov Y, Kolosvari I, Perez A, Dill K, Kozakov D. Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. Journal of Computer-Aided Molecular Design. PMID 30421350 DOI: 10.1007/S10822-018-0176-0  0.6
2018 Stasyk OG, Denega IO, Padhorny D, Dmytruk KV, Kozakov D, Abbas C, Stasyk OV. Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1. The International Journal of Biochemistry & Cell Biology. 103: 25-34. PMID 30081098 DOI: 10.1016/j.biocel.2018.08.002  0.6
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  1
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  1
2017 Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. Plos Computational Biology. 13: e1005905. PMID 29281622 DOI: 10.1371/Journal.Pcbi.1005905  0.8
2017 Padhorny D, Hall DR, Mirzaei H, Mamonov AB, Moghadasi M, Alekseenko A, Beglov D, Kozakov D. Protein-ligand docking using FFT based sampling: D3R case study. Journal of Computer-Aided Molecular Design. PMID 29101520 DOI: 10.1007/S10822-017-0069-7  1
2017 Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, Kozakov D. ClusPro PeptiDock: Efficient global docking of peptide recognition motifs using FFT. Bioinformatics (Oxford, England). PMID 28430871 DOI: 10.1093/Bioinformatics/Btx216  0.92
2017 Bohnuud T, Jones G, Schueler-Furman O, Kozakov D. Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server. Methods in Molecular Biology (Clifton, N.J.). 1561: 11-20. PMID 28236230 DOI: 10.1007/978-1-4939-6798-8_2  0.92
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  1
2016 Marcu O, Dodson EJ, Alam N, Sperber M, Kozakov D, Lensink MF, Schueler-Furman O. FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. Proteins. PMID 28002624 DOI: 10.1002/prot.25230  0.8
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  1
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  1
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  1
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  1
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  1
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, ... ... Kozakov D, 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  1
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  1
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  1
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  1
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  1
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  1
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  1
2015 Alam N, Lavi A, London N, Raveh B, Kozakov D, Schueler-Furman O. 180 Towards the high-resolution, ab initio modeling of peptide-mediated interactions. Journal of Biomolecular Structure & Dynamics. 33: 117-8. PMID 26103390 DOI: 10.1080/07391102.2015.1032817  0.8
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  1
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  1
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  1
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  1
2015 Kazennov AM, Alekseenko AE, Kozakov D, Padhorny DN, Kholodov YA. Efficient search for the possible mutual arrangements of two rigid bodies with the use of the generalized five-dimensional Fourier transform Mathematical Models and Computer Simulations. 7: 315-322. DOI: 10.1134/S2070048215040043  1
2015 Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. Correction for "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: E3749. DOI: 10.1073/pnas.1511466112  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2014 Yakubovskaya E, Guja KE, Eng ET, Choi WS, Mejia E, Beglov D, Lukin M, Kozakov D, Garcia-Diaz M. Organization of the human mitochondrial transcription initiation complex. Nucleic Acids Research. 42: 4100-12. PMID 24413562 DOI: 10.1093/Nar/Gkt1360  1
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, ... ... Kozakov D, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  1
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  1
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  1
2013 Lavi A, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D, Schueler-Furman O, Kozakov D. Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions. Proteins. 81: 2096-105. PMID 24123488 DOI: 10.1002/Prot.24422  1
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  1
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, ... ... Kozakov D, 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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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 (2011) 108, 3, (1046-1051) DOI: 10.1073/pnas. 1011477108) Proceedings of the National Academy of Sciences of the United States of America. 108: 6689. DOI: 10.1073/pnas.1104339108  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
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  1
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  1
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  1
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