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

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 4distance 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 ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Vladimir Potapov, Mati Cohen, Yuval Inbar, Gideon Schreiber
• Keywords: BMCBI 2010, Decoy, Protein, Protein Structures