3 years ago

OPUS-CSF: A C-atom-based Scoring Function for Ranking Protein Structural Models

Jianpeng Ma, Gang Xu, Qinghua Wang, Tianwu Zang, Tianqi Ma
We report a C-atom-based scoring function, named OPUS-CSF, for ranking protein structural models. Rather than using traditional Boltzmann formula, we built a scoring function (CSF score) based on the native distributions (derived from the entire PDB) of coordinate components of mainchain C (carbonyl) atoms on selected residues of peptide segments of 5, 7, 9, and 11 residues in length. In testing OPUS-CSF on decoy recognition, it maximally recognized 257 native structures out of 278 targets in 11 commonly used decoy sets, significantly more than other popular all-atom empirical potentials. The average correlation coefficient with TM-score was also comparable with those of other potentials. OPUS-CSF is a highly coarse-grained scoring function, which only requires input of partial mainchain information, and very fast. Thus it is suitable for applications at early stage of structural building. This article is protected by copyright. All rights reserved.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/pro.3327

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