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. 2020 Aug;88(8):1055-1069.
doi: 10.1002/prot.25874. Epub 2020 Feb 7.

Challenges and opportunities of automated protein-protein docking: HDOCK server vs human predictions in CAPRI Rounds 38-46

Yumeng Yan  1 , Jiahua He  1 , Yuyu Feng  1 , Peicong Lin  1 , Huanyu Tao  1 , Sheng-You Huang  1
Affiliations

Challenges and opportunities of automated protein-protein docking: HDOCK server vs human predictions in CAPRI Rounds 38-46

Yumeng Yan et al. Proteins. 2020 Aug.

Abstract

Protein-protein docking plays an important role in the computational prediction of the complex structure between two proteins. For years, a variety of docking algorithms have been developed, as witnessed by the critical assessment of prediction interactions (CAPRI) experiments. However, despite their successes, many docking algorithms often require a series of manual operations like modeling structures from sequences, incorporating biological information, and selecting final models. The difficulties in these manual steps have significantly limited the applications of protein-protein docking, as most of the users in the community are nonexperts in docking. Therefore, automated docking like a web server, which can give a comparable performance to human docking protocol, is pressingly needed. As such, we have participated in the blind CAPRI experiments for Rounds 38-45 and CASP13-CAPRI challenge for Round 46 with both our HDOCK automated docking web server and human docking protocol. It was shown that our HDOCK server achieved an "acceptable" or higher CAPRI-rated model in the top 10 submitted predictions for 65.5% and 59.1% of the targets in the docking experiments of CAPRI and CASP13-CAPRI, respectively, which are comparable to 66.7% and 54.5% for human docking protocol. Similar trends can also be observed in the scoring experiments. These results validated our HDOCK server as an efficient automated docking protocol for nonexpert users. Challenges and opportunities of automated docking are also discussed.

Keywords: CAPRI; HDOCK; automated docking; protein-protein docking; scoring function; template-based docking.

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REFERENCES

    1. Wodak SJ, Janin J. Computer analysis of protein-protein interaction. J Mol Biol. 1978;124:323-342.
    1. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res. 2000;28:235-242.
    1. Huang S-Y. Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discov Today. 2014;19:1081-1096.
    1. Vajda S, Hall DR, Kozakov D. Sampling and scoring: a marriage made in heaven. Proteins. 2013;81:1874-1884.
    1. Vakser IA. Protein-protein docking: from interaction to interactome. Biophys J. 2014;107:1785-1793.

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