Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking.

[Huang Lab]   [HDOCK]   [Help]   [Output example]  
Input Receptor Molecule using ONE of the following four options: [help]
Input Ligand Molecule using ONE of the following four options: [help]
    Template-free docking   [Explanation]
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Option I: Specify the residues of the binding site.


  1. Yan Y, Zhang D, Zhou P, Li B, Huang S-Y. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res 2017; doi: 10.1093/nar/gkx407.
  2. Yan Y, Wen Z, Wang X, Huang S-Y. Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking. Proteins 2017;85:497-512.
  3. Huang SY, Zou X. A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Res. 2014;42:e55.
  4. Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579.
If you submit sequences, please also cite:
  1. Remmert M, Biegert A, Hauser A, Soing J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 2011;9:173-175.
  2. W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
  3. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.
  4. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947-8.
  5. Marti-Renom MA, Stuart A, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000;29:291-325.
  6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
The PDB database is updated monthly. Current version: 2017-09-02
huanglab@hust.edu.cn, Lab of Biophysics and Molecular Modeling