Format

Send to

Choose Destination
Proteins. 2016 Sep;84 Suppl 1:105-17. doi: 10.1002/prot.24920. Epub 2015 Sep 22.

Protein structure prediction using residue- and fragment-environment potentials in CASP11.

Author information

1
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47906.
2
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47906. dkihara@purdue.edu.
3
Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907. dkihara@purdue.edu.

Abstract

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.

KEYWORDS:

CASP11; decoy selection; helix interaction; knowledge-based potential; protein structure prediction; residue environments; scoring functions

PMID:
26344195
PMCID:
PMC4781684
DOI:
10.1002/prot.24920
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Wiley Icon for PubMed Central
Loading ...
Support Center