Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions.

ABSTRACT:

Background

Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design.

Results

Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter rank

SUBMITTER: Potapov V 

PROVIDER: S-EPMC2912888 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature