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. 2019 Jun 3;20(1):299.
doi: 10.1186/s12859-019-2898-y.

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

Zhongwang Yu  1 , Yuangen Yao  1 , Haiyou Deng  2   3 , Ming Yi  4   5
Affiliations

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

Zhongwang Yu et al. BMC Bioinformatics. .

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/ .

Keywords: Distance cutoff; Pair-wise interaction; Protein decoy set; Protein structure prediction; Statistical potential.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The flowchart of our studies. Step 1. PDB dataset preparation; Step 2. Potential derivation; Step 3. Benchmark test
Fig. 2
Fig. 2
Effects of distance cutoff on ANDIS’s performance. The results are averaged over all 632 structural decoy sets. “angle only” refers to the pure angle potential without involvement of “effective atomic interaction” and distance-dependent atom-pair potential. Since lower energy score (higher TM-score) is desired, the value of PCC is negative, the lower the better
Fig. 3
Fig. 3
Overall effects of dataset size on ANDIS’s performance. ANDIS is re-extracted based on different number of structures from the original dataset (3519 structures)
Fig. 4
Fig. 4
The protein size and MolProbity score for native structures in CASP10-13 decoy sets. ANDIS recognized 129 (out of 175) native structures in CASP10-13 decoy sets. The 46 unrecognized native structures are highlighted by shade open circles
See this image and copyright information in PMC

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