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The HDOCK server for integrated protein–protein docking

Nature Protocols volume 15, pages 1829–1852 (2020)Cite this article

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Abstract

The HDOCK server (http://hdock.phys.hust.edu.cn/) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information incorporation and job management for robust and fast protein–protein docking. With input information for receptor and ligand molecules (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which experimental information about the protein–protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein–RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two molecules and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min.

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Fig. 1: Procedure of the HDOCK server.
Fig. 2: Performance of the HDOCK approach and other docking servers/methods on different categories of targets in the CASP13-CAPRI assembly challenge in 2018.
Fig. 3: Examples of SAXS data with their best predicted models for the top 10 predictions.
Fig. 4: Home screen of the HDOCK server.
Fig. 5: Expanded interface for providing the residues of the binding site.
Fig. 6: HDOCK result page.

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Data availability

The raw data and example files can be downloaded on our HDOCK server (http://hdock.phys.hust.edu.cn/) or are available from the corresponding author upon request.

Code availability

The HDOCK service is freely available for academic use at http://hdock.phys.hust.edu.cn/.

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Acknowledgements

This work was 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 Huazhong University of Science and Technology.

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  1. These authors contributed equally: Yumeng Yan, Huanyu Tao.

Authors and Affiliations

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

    Yumeng Yan, Huanyu Tao, Jiahua He & Sheng-You Huang

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  1. Yumeng Yan
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Contributions

S.-Y.H. conceived and supervised the project. Y.Y., H.T., J.H. and S.-Y.H. designed and performed the experiments. Y.Y., H.T., J.H. and S.-Y.H. wrote the manuscript.

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Correspondence to Sheng-You Huang.

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Related links

Key references using this protocol

Yan, Y. et al. Nucleic Acids Res. 45, W365–W373 (2017): https://doi.org/10.1093/nar/gkx407

Yan, Y. et al. Proteins 85, 497–512 (2017): https://doi.org/10.1002/prot.25234

Yan, Y. et al. Nucleic Acids Res. 46, W423–W431 (2018): https://doi.org/10.1093/nar/gky398

Yan, Y. and Huang, S.-Y. BMC Bioinformatics 20(Suppl 25), 696 (2019): https://doi.org/10.1186/s12859-019-3270-y

Integrated supplementary information

Supplementary Fig. 1 Template-free docking example.

The HDOCK results for template-free docking with target 1CGI, in which sequences were provided as inputs and the template-free docking option was checked.

Supplementary Fig. 2 Symmetric multimer docking example.

The HDOCK results for symmetric multimer docking with D2 target 1HCJ, in which sequences were provided for template-free docking.

Supplementary Fig. 3 SAXS-assisted docking example.

The HDOCK results for SAXS-assisted template-free docking with target 1CGI, in which sequences and SAXS data were provided.

Supplementary Fig. 4 Interaction restraint-guided docking example.

The HDOCK results for interaction restraint-guided template-free docking with target 1CGI, in which residue distance restraints and sequences were provided for docking.

Supplementary Fig. 5 Protein–RNA docking example.

The HDOCK results for template-based modeling and template-free docking with protein–RNA target 1C0A, in which individual structures were provided as inputs.

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Yan, Y., Tao, H., He, J. et al. The HDOCK server for integrated protein–protein docking. Nat Protoc 15, 1829–1852 (2020). https://doi.org/10.1038/s41596-020-0312-x

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