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

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

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

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

Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking.
Totrov M, J Comput Chem, 2004 Mar - 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

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