Summary: A new method for ligand docking to flexible receptors
by dual alanine scanning and refinement (SCARE)
Giovanni Bottegoni Æ Irina Kufareva Æ
Maxim Totrov Æ Ruben Abagyan
Received: 18 December 2007 / Accepted: 23 January 2008 / Published online: 14 February 2008
Ó Springer Science+Business Media B.V. 2008
Abstract Protein binding sites undergo ligand specific
conformational changes upon ligand binding. However,
most docking protocols rely on a fixed conformation of the
receptor, or on the prior knowledge of multiple confor-
mations representing the variation of the pocket, or on a
known bounding box for the ligand. Here we described a
general induced fit docking protocol that requires only one
initial pocket conformation and identifies most of the cor-
rect ligand positions as the lowest score. We expanded a
previously used diverse ``cross-docking'' benchmark to
thirty ligand­protein pairs extracted from different crystal
structures. The algorithm systematically scans pairs of
neighbouring side chains, replaces them by alanines, and
docks the ligand to each `gapped' version of the pocket. All

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego

Collections: Biology and Medicine