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

Proteins
Hyungrae Kim, Daisuke Kihara

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. © 2015 Wiley Periodicals, Inc.

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Citations

Jun 17, 2016·Bioinformatics·Michal JamrozDaisuke Kihara
Jun 23, 2016·Chemical Reviews·Sebastian KmiecikAndrzej Kolinski
Aug 27, 2016·Briefings in Bioinformatics·Dukka B Kc
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Nov 21, 2019·Bioinformatics·Xiao WangDaisuke Kihara
Nov 8, 2019·Proteins·Charles ChristofferDaisuke Kihara
Jun 12, 2021·Frontiers in Molecular Biosciences·Xiao WangDaisuke Kihara
Dec 4, 2019·Journal of Chemical Information and Modeling·Jan Walther Perthold, Chris Oostenbrink

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