Papers+Conferences

2018
Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN, Kozakov D, Whitty A, Vajda S.  2018.  Exploring the structural origins of cryptic sites on proteins. Proceedings of the National Academy of Sciences. 5428138365835429Chap 2:201711490.
2017
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S.  2017.  The ClusPro web server for protein–protein docking. Nature Protocols. 12(2):255-278. Download: PDF (4.46 MB)
Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D.  2017.  New additions to the ClusPro server motivated by CAPRI. Proteins: Structure, Function, and Bioinformatics. 85(3):435-444. Download: PDF (248.38 KB)
Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S.  2017.  ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking. Journal of Molecular Biology. 429(3):372-381. Download: PDF (743.59 KB)
2016
2015
Vajda S, Whitty A, Kozakov D.  2015.  Fragments and hot spots in drug discovery. Oncotarget. 6(22):18740-18741. Download: PDF (504.45 KB)
Hall DR, Kozakov D, Whitty A, Vajda S.  2015.  Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.. Trends in Pharmacological Sciences. 36(11):724-36. Download: PDF (2.27 MB)
Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S.  2015.  New Frontiers in Druggability. Journal of Medicinal Chemistry. :150811124427009. Download: PDF (9.06 MB)
Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis IC, Vakili P, Kozakov D.  2015.  Energy Minimization on Manifolds for Docking Flexible Molecules. Journal of Chemical Theory and Computation. 11(3):1063-1076. Download: PDF (5.51 MB)
Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S, Paschalidis IC, Kozakov D.  2015.  The Impact of Side-Chain Packing on Protein Docking Refinement. Journal of Chemical Information and Modeling. :150324100758004. Download: PDF (3.53 MB)
Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S.  2015.  Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proceedings of the National Academy of Sciences. :201501567. Download: PDF (1003.22 KB)
2014
Villar EA, Beglov D, Chennamadhavuni S, Porco JA, Kozakov D, Vajda S, Whitty A.  2014.  How proteins bind macrocycles. Nature Chemical Biology.  Download: PDF (1.17 MB)
Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P, Vajda S, Bajaj C, Kozakov D.  2014.  Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations. Journal of Chemical Theory and Computation. :140926082652006. Download: PDF (2.01 MB)
Mottarella SE, Beglov D, Beglova N, Nugent MA, Kozakov D, Vajda S.  2014.  Docking Server for the Identification of Heparin Binding Sites on Proteins. Journal of Chemical Information and Modeling. 54(7):2068-2078. Download: PDF (3.97 MB)
Vakili P, Mirzaei H, Zarbafian S, Paschalidis IC, Kozakov D, Vajda S.  2014.  Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. 2014 IEEE 53rd Annual Conference on Decision and Control (CDC)53rd IEEE Conference on Decision and Control. :5825-5830. Download: PDF (473.3 KB)
2013
Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S.  2013.  How good is automated protein docking? Proteins: Structure, Function, and Bioinformatics.  Download: PDF (207.49 KB)
Vajda S, Hall DR, Kozakov D.  2013.  Sampling and scoring: A marriage made in heaven. Proteins: Structure, Function, and Bioinformatics.  Download: PDF (212.68 KB)
Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E, Schmitz C, van Dijk M, Bonvin AMJJ, Eisenstein M et al..  2013.  Blind prediction of interfacial water positions in CAPRI. Proteins: Structure, Function, and Bioinformatics. 82(4):620-632. Download: PDF (554.23 KB)
Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P.  2013.  Flexible refinement of protein-ligand docking on manifolds. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :1392-1397. Download: PDF (384.37 KB)
Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC.  2013.  A new distributed algorithm for side-chain positioning in the process of protein docking. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :739-744. Download: PDF (334.84 KB)
2012
Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D.  2012.  Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.. Journal of chemical information and modeling.  Download: PDF (3.75 MB)
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.  2012.  Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. 8(11):4374-4380.
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.  2012.  Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. :120821123549006. Download: PDF (317.26 KB)
Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S.  2012.  FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Research. 40(W1):W271-W275. Download: PDF (1.33 MB)
Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL, Kozakov D, Vajda S.  2012.  Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins: Structure, Function, and Bioinformatics. 80(2):591-601. Download: PDF (1.57 MB)
Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S.  2012.  Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling. 52(1):199-209. Download: PDF (1.92 MB)
Hall DR, Kozakov D, Vajda S.  2012.  Analysis of Protein Binding Sites by Computational Solvent Mapping. Methods in Molecular Biology. 819:13-27. Download: PDF (1.71 MB)
Moghadasi M, Kozakov D, Mamonov AB, Vakili P, Vajda S, Paschalidis IC.  2012.  A message passing approach to Side Chain Positioning with applications in protein docking refinement. 2012 IEEE 51st Annual Conference on Decision and Control (CDC)2012 IEEE 51st IEEE Conference on Decision and Control (CDC). :2310-2315.
Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P.  2012.  A new approach to rigid body minimization with application to molecular docking. 2012 IEEE 51st Annual Conference on Decision and Control (CDC)2012 IEEE 51st IEEE Conference on Decision and Control (CDC). :2983-2988.
2011
Hall DR, Grove LE, Yueh C, Ngan CH, Kozakov D, Vajda S.  2011.  Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme. Journal of the American Chemical Society. 133(51):20668-20671. Download: PDF (3.55 MB)
Kozakov D, Hall DR, Chuang G-Y, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S.  2011.  Structural conservation of druggable hot spots in protein-protein interfaces. Proceedings of the National Academy of Sciences. 108(33):13528-13533. Download: PDF (7.25 MB)
Cencic R, Hall DR, Robert F, Du Y, Min J, Li L, Qui M, Lewis I, Kurtkaya S, Dingledine R et al..  2011.  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(3):1046-51. Download: PDF (2.42 MB)
2010
2009
Ngan CH, Beglov D, Rudnitskaya AN, Kozakov D, Waxman DJ, Vajda S.  2009.  The Structural Basis of Pregnane X Receptor Binding Promiscuity. Biochemistry. 48(48):11572-11581. Download: PDF (3.14 MB)
Beglov D, Lee C-J, De Biasio A, Kozakov D, Brenke R, Vajda S, Beglova N.  2009.  Structural insights into recognition of β2-glycoprotein I by the lipoprotein receptors. Proteins: Structure, Function, and Bioinformatics. 77(4):940-949. Download: PDF (419.27 KB)
Vajda S, Kozakov D.  2009.  Convergence and combination of methods in protein–protein docking. Current Opinion in Structural Biology. 19(2):164-170. Download: PDF (250.8 KB)
2008
2007
Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S.  2007.  ClusPro: Performance in CAPRI rounds 6–11 and the new server. Proteins: Structure, Function, and Bioinformatics. 69(4):781-785. Download: PDF (213.15 KB)
Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S.  2007.  Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI. Proteins: Structure, Function, and Bioinformatics. 69(4):734-742. Download: PDF (274.39 KB)
2006
Kozakov D, Brenke R, Comeau SR, Vajda S.  2006.  PIPER: An FFT-based protein docking program with pairwise potentials. Proteins: Structure, Function, and Bioinformatics. 65(2):392-406. Download: PDF (385.54 KB)
2005