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Soft proteinprotein docking in internal coordinates JUAN FERNA NDEZ-RECIO,1
 

Summary: Soft protein­protein docking in internal coordinates
JUAN FERNA´ NDEZ-RECIO,1
MAXIM TOTROV,2
AND RUBEN ABAGYAN1
1
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
2
Molsoft, LLC, La Jolla, Calfornia 92037, USA
(RECEIVED May 22, 2001; FINAL REVISION October 12, 2001; ACCEPTED November 2, 2001)
Abstract
The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved
theoretical problem. Docking methods for ab initio prediction of association of two independently deter-
mined protein structures usually fail when they are applied to a large set of complexes, mostly because of
inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface
residues on binding. In this work we present an efficient pseudo-Brownian rigid-body docking procedure
followed by Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. The use of
a soft interaction energy function precalculated on a grid, instead of the explicit energy, drastically increased
the speed of the procedure. The method was tested on a benchmark of 24 protein­protein complexes in
which the three-dimensional structures of their subunits (bound and free) were available. The rank of the
near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no

  

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

 

Collections: Biology and Medicine