A pairwise residue contact area-based mean force potential for discrimination of native protein structure.

ABSTRACT:

Background

Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed.

Results

We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy

SUBMITTER: Arab S 

PROVIDER: S-EPMC2821318 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature