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A simplified amino acid potential for use in structure predictions of proteins
Author(s) -
Wallqvist A.,
Ullner M.
Publication year - 1994
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.340180308
Subject(s) - amino acid residue , folding (dsp implementation) , chemistry , side chain , amino acid , parameterized complexity , hydrogen bond , monte carlo method , force field (fiction) , residue (chemistry) , statistical physics , crystallography , chemical physics , physics , molecule , algorithm , peptide sequence , computer science , mathematics , biochemistry , organic chemistry , statistics , quantum mechanics , electrical engineering , gene , engineering , polymer
ABSTRACT A simplified description and a corresponding force field for polypeptides is introduced. Each amino acid residue is reduced to one interaction site, representing the backbone, and one or two side chain sites depending on its size and complexity. Site–site interactions are parameterized after a hydrophobicity criterium. The treatment of backbone sites is in addition designed to reproduce typical polypeptide hydrogen bonding patterns, as well as yielding conformations in accord with the allowed ϕ and ψ angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, which are based on thermodynamic data and sterical consideration of allowed backbone conformations, correspond to the introduction of an effective potential. The model is tested on two small proteins, avian pancreatic polypeptide and a parathyroid hormone‐related protein, by simulating folding from an initially extended state using Monte Carlo methods. The reduced amino acid description is able to satisfactorily reproduce the experimentally determined native structures. © 1994 John Wiley & Sons, Inc.