Amino acid empirical contact energy definitions for fold recognition in the space of contact maps.

ABSTRACT: BACKGROUND:Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of information available from selected protein structures, with respect to a defined reference state, according to the quasi-chemical approximation. Protein-solvent interactions are estimated from residue solvent accessibility. RESULTS:In the approach presented here, contact energies are derived from the potential of mean force theory, several definitions of contact are examined and their performance in fold recognition is evaluated on sets of decoy structures. The best definition of contact is tested, on a more realistic scenario, on all predictions including sidechains accepted in the

SUBMITTER: Berrera M 

PROVIDER: S-EPMC153506 | biostudies-literature | 2003 Feb

REPOSITORIES: biostudies-literature