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

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


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.

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

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenoviridae / chemistry
  • Algorithms
  • Computational Biology / methods
  • Computational Biology / statistics & numerical data*
  • Databases, Protein
  • Humans
  • Internet
  • Models, Statistical*
  • Molecular Dynamics Simulation*
  • Protein Folding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Research Design
  • Software*


  • Proteins