Structural
BioinformaticsLab

Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA, Beglov D, Sazinsky SL, Georgiadis RM, Vajda S, Kozakov D et al..  2013.  Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator (NEMO)/IKKβ Protein-Protein Interface. Journal of the American Chemical Society. :130318121200001. Download: PDF (3.15 MB)

Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo J-L, Dash R, Sarkar D, Hall DR, Kozakov D, Vajda S et al..  2012.  A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy. PLoS ONE. 7(7):e40234. Download: PDF (1.67 MB)

Zerbe B, 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. :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)

Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, Vajda S.  2012.  FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics. 28(2):286-287. Download: PDF (268.3 KB)

Hall DR, Ngan CH, Zerbe B, 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)

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)

Buhrman G, O′Connor C, Zerbe B, Kearney BM, Napoleon R, Kovrigina EA, Vajda S, Kozakov D, Kovrigin EL, Mattos C.  2011.  Analysis of Binding Site Hot Spots on the Surface of Ras GTPase. Journal of Molecular Biology. 413(4):773-789.

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, Desforges M, Hall DR, Kozakov D, Du Y, Min J, Dingledine R, Fu H, Vajda S, Talbot PJ et al..  2011.  Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication. Journal of Virology. 85(13):6381-6389. Download: PDF (2.21 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. Abstract  Download: PDF (2.42 MB)

Chuang G-Y, Mehra-Chaudhary R, Ngan CH, Zerbe B, Kozakov D, Vajda S, Beamer LJ.  2010.  Domain motion and inter-domain hot spots in a multi-domain enzyme. Protein Science.  Download: PDF (403.54 KB)

Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis IC et al..  2010.  Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins: Structure, Function, and Bioinformatics. 78(15):3124-3130. Download: PDF (297.68 KB)

Kozakov D, Chuang G-Y, Beglov D, Vajda S.  2010.  Where does amantadine bind to the influenza virus M2 proton channel? Trends in Biochemical Sciences.  Download: PDF (263.58 KB)

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)

Chuang G-Y, Kozakov D, Brenke R, Beglov D, Guarnieri F, Vajda S.  2009.  Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel. Biophysical Journal. 97(10):2846-2853. Download: PDF (514.97 KB)

Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JMM, Orwig SD, Kozakov D, Brenke R, Chuang G-Y, Beglov D et al..  2009.  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(8):491-500. Download: PDF (574.15 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)

Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall DR, Landon MR, Mattos C, Vajda S.  2009.  Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics. 25(5):621-627. Download: PDF (412.04 KB)

Beglov D, Brenke R, Chuang G-Y, Hall DR, Landon MR, Ngan CH, Shen Y, Thiel SC, Zerbe B, Kozakov D et al..  2009.  Identification of Druggable Hot Spots on Proteins and in Protein Protein Interfaces. Computational Protein-Protein Interactions.

Chuang G-Y, Kozakov D, Brenke R, Comeau SR, Vajda S.  2008.  DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking. Biophysical Journal. 95(9):4217-4227. Download: PDF (317.38 KB)

Kozakov D, Schueler‐Furman O, Vajda S.  2008.  Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima. Proteins: Structure, Function, and Bioinformatics. 72(3):993-1004. Download: PDF (328.1 KB)

Ritchie DW, Kozakov D, Vajda S.  2008.  Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics. 24(17):1865-1873. Download: PDF (328.1 KB)

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)

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)

Kozakov D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformations in Protein Docking. Biophysical Journal. 89(2):867-875. Download: PDF (326.16 KB)

Kozakov D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformation in Protein Docking. CAPRI Meeting.  Download: PPT (5.34 MB)