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Lattice Protein Folding with Two and Four-body Statistical Potentials by Hin Hark Gan; Alexander Tropsha; Tamar Schlick is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Lattice Protein Folding with Two and Four-body Statistical Potentials about?

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 fourbody 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-␣ 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, bu

Who reads Lattice Protein Folding with Two and Four-body Statistical Potentials?

Author

Hin Hark Gan; Alexander Tropsha; Tamar Schlick

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2001

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)