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

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