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Monte Carlo docking of oligopeptides to proteins
Author(s) -
Caflisch Amedeo,
Niederer Peter,
Anliker Max
Publication year - 1992
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340130305
Subject(s) - docking (animal) , searching the conformational space for docking , monte carlo method , oligopeptide , chemistry , protein–ligand docking , crystallography , molecule , protein structure , molecular dynamics , biological system , stereochemistry , peptide , computational chemistry , biochemistry , mathematics , biology , virtual screening , organic chemistry , medicine , statistics , nursing
A new two‐step procedure has been developed for the docking of flexible oligopeptide chains of unkown conformation to static proteins ofknown structure. In the first step positions and conformations are sampled and the association energy, minimized starting from an approximate preselected docking position. The resulting conformations are further optimized in the second step by a Metropolis Monte Carlo minimization, which optimizes each of these structures. The method has been tested on the HIV‐1 aspartic proteinase complex with an inhibitor, whose crystallographic structure is known at 2.3 Å resolution. Furthermore, the application of this method to the docking of the hendecapeptide 58–68 of the influenza A virus matrix protein to the HLA‐A2 molecule produced results which are in agreement with experimental observations in identifying side chains critical for T cell recognition and residues responsible of MHC protein binding. © 1992 Wiley‐Liss, Inc.