Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2020 May;15(5):1829-1852.
doi: 10.1038/s41596-020-0312-x. Epub 2020 Apr 8.

The HDOCK server for integrated protein-protein docking

Yumeng Yan #  1 , Huanyu Tao #  1 , Jiahua He  1 , Sheng-You Huang  2
Affiliations
Comparative Study

The HDOCK server for integrated protein-protein docking

Yumeng Yan et al. Nat Protoc. 2020 May.

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.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000). - PubMed - PMC
    1. Vajda, S., Hall, D. R. & Kozakov, D. Sampling and scoring: a marriage made in heaven. Proteins 81, 1874–1884 (2013). - PubMed
    1. Vakser, I. A. Protein-protein docking: from interaction to interactome. Biophys. J. 107, 1785–1793 (2014). - PubMed - PMC
    1. Huang, S. Y. Exploring the potential of global protein-protein docking: an overview and critical assessment of current programs for automatic ab initio docking. Drug Discov. Today 20, 969–977 (2015). - PubMed
    1. Huang, S. Y. Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discov. Today 19, 1081–1096 (2014). - PubMed

Publication types

MeSH terms

LinkOut - more resources