ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment

BMC Bioinformatics

Zhongwang Yu¹  Ming Yi¹  Yuangen Yao¹  Haiyou Deng¹ 

[1] Department of Physics, College of Science, Huazhong Agricultural University;

关键词: Statistical potential;    Pair-wise interaction;    Protein decoy set;    Distance cutoff;    Protein structure prediction;   

DOI  :  10.1186/s12859-019-2898-y

来源: DOAJ

【 摘 要 】

Abstract Background The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as decoy discrimination. However, these two aspects are found to be mutually exclusive in many statistical potentials. Results We developed an atomic ANgle- and DIStance-dependent (ANDIS) statistical potential for protein structure quality assessment with distance cutoff being a tunable parameter. When distance cutoff is ≤9.0 Å, “effective atomic interaction” is employed to enhance the ability of native recognition. For a distance cutoff of ≥10 Å, the distance-dependent atom-pair potential with random-walk reference state is combined to strengthen the ability of decoy discrimination. Benchmark tests on 632 structural decoy sets from diverse sources demonstrate that ANDIS outperforms other state-of-the-art potentials in both native recognition and decoy discrimination. Conclusions Distance cutoff is a crucial parameter for distance-dependent statistical potentials. A lower distance cutoff is better for native recognition, while a higher one is favorable for decoy discrimination. The ANDIS potential is freely available as a standalone application at http://qbp.hzau.edu.cn/ANDIS/.

【 授权许可】

Unknown