|The ClusPro web server for protein–protein docking|
D Kozakov, DR Hall, B Xia, KA Porter, D Padhorny, C Yueh, D Beglov, ...
Nature protocols 12 (2), 255-278, 2017
|PIPER: an FFT‐based protein docking program with pairwise potentials|
D Kozakov, R Brenke, SR Comeau, S Vajda
Proteins: Structure, Function, and Bioinformatics 65 (2), 392-406, 2006
|How good is automated protein docking?|
D Kozakov, D Beglov, T Bohnuud, SE Mottarella, B Xia, DR Hall, S Vajda
Proteins: Structure, Function, and Bioinformatics 81 (12), 2159-2166, 2013
|Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques|
R Brenke, D Kozakov, GY Chuang, D Beglov, D Hall, MR Landon, ...
Bioinformatics 25 (5), 621-627, 2009
|The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins|
D Kozakov, LE Grove, DR Hall, T Bohnuud, SE Mottarella, L Luo, B Xia, ...
Nature protocols 10 (5), 733-755, 2015
|How proteins bind macrocycles|
EA Villar, D Beglov, S Chennamadhavuni, JA Porco, D Kozakov, S Vajda, ...
Nature chemical biology 10 (9), 723-731, 2014
|New additions to the C lus P ro server motivated by CAPRI|
S Vajda, C Yueh, D Beglov, T Bohnuud, SE Mottarella, B Xia, DR Hall, ...
Proteins: Structure, Function, and Bioinformatics 85 (3), 435-444, 2017
|Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19|
D Kozakov, DR Hall, D Beglov, R Brenke, SR Comeau, Y Shen, K Li, ...
Proteins: Structure, Function, and Bioinformatics 78 (15), 3124-3130, 2010
|Convergence and combination of methods in protein–protein docking|
S Vajda, D Kozakov
Current opinion in structural biology 19 (2), 164-170, 2009
|Structural conservation of druggable hot spots in protein–protein interfaces|
D Kozakov, DR Hall, GY Chuang, R Cencic, R Brenke, LE Grove, ...
Proceedings of the National Academy of Sciences 108 (33), 13528-13533, 2011
|Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions|
DW Ritchie, D Kozakov, S Vajda
Bioinformatics 24 (17), 1865-1873, 2008
|Allostery in its many disguises: from theory to applications|
SJ Wodak, E Paci, NV Dokholyan, IN Berezovsky, A Horovitz, J Li, ...
Structure 27 (4), 566-578, 2019
|Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F|
R Cencic, DR Hall, F Robert, Y Du, J Min, L Li, M Qui, I Lewis, S Kurtkaya, ...
Proceedings of the National Academy of Sciences 108 (3), 1046-1051, 2011
|Ligand Binding and Activation of PPARγ by Firemaster® 550: Effects on Adipogenesis and Osteogenesis in Vitro|
HK Pillai, M Fang, D Beglov, D Kozakov, S Vajda, HM Stapleton, ...
Environmental health perspectives 122 (11), 1225-1232, 2014
|FTSite: high accuracy detection of ligand binding sites on unbound protein structures|
CH Ngan, DR Hall, B Zerbe, LE Grove, D Kozakov, S Vajda
Bioinformatics 28 (2), 286-287, 2012
|Analysis of binding site hot spots on the surface of Ras GTPase|
G Buhrman, O Casey, B Zerbe, BM Kearney, R Napoleon, EA Kovrigina, ...
Journal of molecular biology 413 (4), 773-789, 2011
|Application of asymmetric statistical potentials to antibody–protein docking|
R Brenke, DR Hall, GY Chuang, SR Comeau, T Bohnuud, D Beglov, ...
Bioinformatics 28 (20), 2608-2614, 2012
|DARS (Decoys As the Reference State) potentials for protein-protein docking|
GY Chuang, D Kozakov, R Brenke, SR Comeau, S Vajda
Biophysical journal 95 (9), 4217-4227, 2008
|Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment|
MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ...
Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016
|Optimal clustering for detecting near-native conformations in protein docking|
D Kozakov, KH Clodfelter, S Vajda, CJ Camacho
Biophysical journal 89 (2), 867-875, 2005