Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys.

ABSTRACT:

Background

For over 30 years potentials of mean force have been used to evaluate the relative energy of protein structures. The most commonly used potentials define the energy of residue-residue interactions and are derived from the empirical analysis of the known protein structures. However, single-body residue 'environment' potentials, although widely used in protein structure analysis, have not been rigorously compared to these classical two-body residue-residue interaction potentials. Here we do not try to combine the two different types of residue interaction potential, but rather to assess their independent contribution to scoring protein structures.

Results

A data set of nearly three thousand monomers was used to compare pairwise residue-residue 'contact-type' propens

SUBMITTER: Bolser DM 

PROVIDER: S-EPMC2642821 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature