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Lattice protein folding with two and four‐body statistical potentials
Author(s) -
Gan Hin Hark,
Tropsha Alexander,
Schlick Tamar
Publication year - 2001
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 - 10.1002/1097-0134(20010501)43:2<161::aid-prot1028>3.0.co;2-f
Subject(s) - statistical potential , protein folding , statistical physics , potential energy , lattice (music) , mathematics , root mean square , rigid body , physics , protein structure , combinatorics , protein structure prediction , classical mechanics , quantum mechanics , nuclear magnetic resonance , acoustics
The cooperative folding of proteins implies a description by multibody potentials. Such multibody potentials can be generalized from common two‐body statistical potentials through a relation to probability distributions of residue clusters via the Boltzmann condition. In this exploratory study, we compare a four‐body statistical potential, defined by the Delaunay tessellation of protein structures, to the Miyazawa–Jernigan (MJ) potential for protein structure prediction, using a lattice chain growth algorithm. We use the four‐body potential as a discriminatory function for conformational ensembles generated with the MJ potential and examine performance on a set of 22 proteins of 30–76 residues in length. We find that the four‐body potential yields comparable results to the two‐body MJ potential, namely, an average coordinate root‐mean‐square deviation (cRMSD) value of 8 Å for the lowest energy configurations of all‐α proteins, and somewhat poorer cRMSD values for other protein classes. For both two and four‐body potentials, superpositions of some predicted and native structures show a rough overall agreement. Formulating the four‐body potential using larger data sets and direct, but costly, generation of conformational ensembles with multibody potentials may offer further improvements. Proteins 2001;43:161–174. © 2001 Wiley‐Liss, Inc.