Protein structure prediction using residue- and fragment-environment potentials in CASP11.
An accurate scoring function that can select near-native structure models from a pool of alternative models is key for successful protein structure prediction. For the critical assessment of techniques for protein structure prediction (CASP) 11, we have built a protocol of protein structure prediction that has novel coarse-grained scoring functions for selecting decoys as the heart of its pipeline. The score named PRESCO (Protein Residue Environment SCOre) developed recently by our group evaluates the native-likeness of local structural environment of residues in a structure decoy considering positions and the depth of side-chains of spatially neighboring residues. We also introduced a helix interaction potential as an additional scoring function for selecting decoys. The best models selected by PRESCO and the helix interaction potential underwent structure refinement, which includes side-chain modeling and relaxation with a short molecular dynamics simulation. Our protocol was successful, achieving the top rank in the free modeling category with a significant margin of the accumulated Z-score to the subsequent groups when the top 1 models were considered. Proteins 2016; 84(Suppl 1):105-117. © 2015 Wiley Periodicals, Inc.
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47906.
Hyungrae
H
Kim
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47906. dkihara@purdue.edu.|Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907. dkihara@purdue.edu.
Daisuke
D
Kihara
D000256:Adenoviridae / Q000737:chemistry; D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012107:Research Design; D012984:Software
D011506:Proteins
CASP11; decoy selection; helix interaction; knowledge-based potential; protein structure prediction; residue environments; scoring functions