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A new pairwise folding potential based on improved decoy generation and side‐chain packing
Author(s) -
Loose C.,
Klepeis J. L.,
Floudas C. A.
Publication year - 2003
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.10521
Subject(s) - decoy , pairwise comparison , folding (dsp implementation) , chain (unit) , computer science , side chain , chemistry , biological system , physics , artificial intelligence , biology , engineering , biochemistry , electrical engineering , receptor , organic chemistry , astronomy , polymer
A new force field for pairwise residue interactions as a function of C α to C α distances is presented. The force field was developed through the solution of a linear programming formulation with large sets of constraints. The constraints are based on the construction of >80,000 low‐energy decoys for a set of proteins and requiring the decoy energies for each protein system to be higher than the native conformation of that particular protein. The generation of a robust force field was facilitated by the use of a novel decoy generation process, which involved the rational selection of proteins to add to the training set and included a significant energy minimization of the decoys. The force field was tested on a large set of decoys for various proteins not included in the training set and shown to perform well compared with a leading force field in identifying the native conformation for these proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.