FRODOCK: a new approach for fast rotational protein-protein docking.
Garzon JI, Lopez-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P, Bioinformatics, 2009 Oct 1 - link

Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling.
Dong M, Lam PC, Pinon DI, Abagyan R, Miller LJ, Biochemistry, 2009 Jun 16 - link

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.
Rueda M, Bottegoni G, Abagyan R, J Chem Inf Model, 2009 Mar - link

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes.
Rueda M, Bottegoni G, Abagyan R, J Chem Inf Model, 2009 Feb 16 - link

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.
Bottegoni G, Kufareva I, Totrov M, Abagyan R, J Med Chem, 2009 Jan 22 - link

Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states.
Kufareva I, Abagyan R, J Med Chem, 2008 Dec 25 - link

Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking.
Ma DL, Lai TS, Chan FY, Chung WH, Abagyan R, Leung YC, Wong KY, ChemMedChem, 2008 Jun - link

Flexible ligand docking to multiple receptor conformations: a practical alternative.
Totrov M, Abagyan R, Curr Opin Struct Biol, 2008 Apr - link

Optimization of high throughput virtual screening by combining shape-matching and docking methods.
Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S, J Chem Inf Model, 2008 Mar - link

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).
Bottegoni G, Kufareva I, Totrov M, Abagyan R, J Comput Aided Mol Des, 2008 May - link

Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.
Medina M, Abagyan R, Gomez-Moreno C, Fernandez-Recio J, Proteins, 2008 Aug 15 - link

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.
Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan R, Hruby DE, J Comput Aided Mol Des, 2007 Oct-Nov - link

Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues.
Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ, J Biol Chem, 2007 Nov 9 - link

Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor.
Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ, Mol Pharmacol, 2007 Aug - link

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.
Garzon JI, Kovacs J, Abagyan R, Chacon P, Bioinformatics, 2007 Feb 15 - link

Improving CAPRI predictions: optimized desolvation for rigid-body docking.
Fernandez-Recio J, Abagyan R, Totrov M, Proteins, 2005 Aug 1 - link

Optimal docking area: a new method for predicting protein-protein interaction sites.
Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R, Proteins, 2005 Jan 1 - link

Comparative study of several algorithms for flexible ligand docking.
Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd, J Comput Aided Mol Des, 2003 Nov - link

Identification of protein-protein interaction sites from docking energy landscapes.
Fernandez-Recio J, Totrov M, Abagyan R, J Mol Biol, 2004 Jan 16 - link

ICM-DISCO docking by global energy optimization with fully flexible side-chains.
Fernandez-Recio J, Totrov M, Abagyan R, Proteins, 2003 Jul 1 - link

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking.
Schapira M, Raaka BM, Das S, Fan L, Totrov M, Zhou Z, Wilson SR, Abagyan R, Samuels HH, Proc Natl Acad Sci U S A, 2003 Jun 10 - link

Screened charge electrostatic model in protein-protein docking simulations.
Fernandez-Recio J, Totrov M, Abagyan R, Pac Symp Biocomput, 2002 - link

Soft protein-protein docking in internal coordinates.
Fernandez-Recio J, Totrov M, Abagyan R, Protein Sci, 2002 Feb - link

High-throughput docking for lead generation.
Abagyan R, Totrov M, Curr Opin Chem Biol, 2001 Aug - link

Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics.
Stigler RD, Hoffmann B, Abagyan R, Schneider-Mergener J, Structure, 1999 Jun 15 - link

Flexible protein-ligand docking by global energy optimization in internal coordinates.
Totrov M, Abagyan R, Proteins, 1997 - link

Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.
Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN, Nat Struct Biol, 1996 Mar - link