Detecting local residue environment similarity for recognizing near-native structure models

Proteins. 2014 Dec;82(12):3255-72. doi: 10.1002/prot.24658. Epub 2014 Oct 30.

Abstract

We developed a new representation of local amino acid environments in protein structures called the Side-chain Depth Environment (SDE). An SDE defines a local structural environment of a residue considering the coordinates and the depth of amino acids that locate in the vicinity of the side-chain centroid of the residue. SDEs are general enough that similar SDEs are found in protein structures with globally different folds. Using SDEs, we developed a procedure called PRESCO (Protein Residue Environment SCOre) for selecting native or near-native models from a pool of computational models. The procedure searches similar residue environments observed in a query model against a set of representative native protein structures to quantify how native-like SDEs in the model are. When benchmarked on commonly used computational model datasets, our PRESCO compared favorably with the other existing scoring functions in selecting native and near-native models.

Keywords: decoy selection; protein local structures; protein structure models; quality assessment; residue depth; residue environment.

Publication types

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

MeSH terms

  • Amino Acids / chemistry*
  • Animals
  • Computer Simulation
  • Energy Transfer
  • Humans
  • Models, Molecular*
  • Protein Conformation*
  • Protein Folding
  • Reproducibility of Results
  • Software Validation
  • Support Vector Machine
  • Surface Properties

Substances

  • Amino Acids