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BMC Bioinformatics. 2017 Dec 8;18(1):542. doi: 10.1186/s12859-017-1983-3.

Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction.

Author information

1
Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
2
Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China. hydeng@mail.hzau.edu.cn.
3
Institute of Applied Physics, Huazhong Agricultural University, Wuhan, 430070, China. hydeng@mail.hzau.edu.cn.

Abstract

BACKGROUND:

As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model refinement, and model assessment. During the last two decades, great efforts have been made to improve the reference state of the potential, while other factors that also strongly affect the performance of the potential have been relatively less investigated.

RESULTS:

Based on different distance cutoffs (from 5 to 22 Å) and residue intervals (from 0 to 15) as well as six different reference states, we constructed a series of distance-dependent atom-pair potentials and tested them on several groups of structural decoy sets collected from diverse sources. A comprehensive investigation has been performed to clarify the effects of distance cutoff and residue interval on the potential's performance. Our results provide a new perspective as well as a practical guidance for optimizing distance-dependent statistical potentials.

CONCLUSIONS:

The optimal distance cutoff and residue interval are highly related with the reference state that the potential is based on, the measurements of the potential's performance, and the decoy sets that the potential is applied to. The performance of distance-dependent statistical potential can be significantly improved when the best statistical parameters for the specific application environment are adopted.

KEYWORDS:

Distance cutoff; Distance-dependent atom-pair potential; Protein structure prediction; Reference state; Residue interval

PMID:
29221443
PMCID:
PMC5723101
DOI:
10.1186/s12859-017-1983-3
[Indexed for MEDLINE]
Free PMC Article

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