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
2016
2015
2014
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)
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)
2012
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)
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
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)
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)
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)