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OPUS‐CSF: A C‐atom‐based scoring function for ranking protein structural models
Author(s) -
Xu Gang,
Ma Tianqi,
Zang Tianwu,
Wang Qinghua,
Ma Jianpeng
Publication year - 2018
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3327
Subject(s) - decoy , ranking (information retrieval) , protein data bank (rcsb pdb) , function (biology) , atom (system on chip) , computer science , chemistry , mathematics , computational biology , biological system , algorithm , bioinformatics , artificial intelligence , biology , stereochemistry , biochemistry , genetics , receptor , embedded system
We report a C ‐atom‐based s coring f unction, 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 outperforming 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.