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Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2165))

Abstract

Protein–protein and protein–DNA/RNA interactions are involved in many cellular processes. Therefore, determining their complex structures at the atomic level is valuable to gain insights into these interactions. Because of the technical difficulties and high cost in experimental methods, computational approaches like molecular docking have been developed to predict the structures of macromolecular complexes in the last decades. To automatically integrate the available binding information from the PDB, we have developed HDOCK, a protein–protein/nucleic acid docking web server by combining template-based and free docking. In this chapter, we first briefly introduce our HDOCK server and then give a step-by-step description of docking bovine chymotrypsinogen A against its inhibitor (PDB ID: 1CGI). Two case studies of realistic examples are also discussed. The HDOCK server is freely available at http://hdock.phys.hust.edu.cn/.

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Acknowledgments

This work is supported by the National Natural Science Foundation of China (grant No. 31670724), the National Key Research and Development Program of China (grant Nos. 2016YFC1305800 and 2016YFC1305805), and the startup grant of the Huazhong University of Science and Technology (grant No. 3004012104).

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Authors and Affiliations

  1. School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China

    Yumeng Yan & Sheng-You Huang

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  1. Yumeng Yan
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  2. Sheng-You Huang
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Correspondence to Sheng-You Huang .

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Editors and Affiliations

  1. Department of Computer Science, Purdue University, West Lafayette, IN, USA

    Daisuke Kihara

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Yan, Y., Huang, SY. (2020). Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_12

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  • DOI: https://doi.org/10.1007/978-1-0716-0708-4_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0707-7

  • Online ISBN: 978-1-0716-0708-4

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