title: Detecting local residue environment similarity for recognizing near-native structure models.
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.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47906.
authors.forename: Hyungrae
authors.initials: H
authors.lastname: Kim
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kihara
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D003198:Computer Simulation; D004735:Energy Transfer; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D015203:Reproducibility of Results; D012986:Software Validation; D060388:Support Vector Machine; D013499:Surface Properties
chemical_list: D000596:Amino Acids
keywords: decoy selection; protein local structures; protein structure models; quality assessment; residue depth; residue environment