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Critical evaluation of the research docking program for the CASP2 challenge
Author(s) -
Hart Trevor N.,
Ness Steven R.,
Read Randy J.
Publication year - 1997
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/(sici)1097-0134(1997)1+<205::aid-prot27>3.0.co;2-r
Subject(s) - docking (animal) , searching the conformational space for docking , pairwise comparison , monte carlo method , non covalent interactions , crystallography , computer science , computational chemistry , molecule , chemistry , statistical physics , physics , protein structure , mathematics , artificial intelligence , hydrogen bond , statistics , nuclear magnetic resonance , medicine , nursing , organic chemistry
The binding positions of six small‐molecule ligands in their complexes with target proteins were predicted using our Research docking program for the CASP2 challenge. Research uses a Monte Carlo procedure with pairwise energies and allows for the conformational searching of ligand torsional space. We were able to predict 2 of the 5 noncovalent complexes within 2 Å root‐mean‐square (RMS) of the experimental structures as ranked by interaction energy or by a score calculated using our interaction evaluation program, Outrank. In addition, for 4 of the 5 noncovalent structures we found a docking within 2 Å RMS of the experimental structure within the top 20 dockings as ranked by energy. The main limitation in our approach is in the ability of the energy function and Outrank to discriminate among the lowest energy dockings. On the other hand, our success in exploring the multidimensional docking space of position, orientation and conformation is encouraging. Proteins, Suppl. 1:205–209, 1997. © 1998 Wiley‐Liss, Inc.