HPEPDOCK 2.0      
[Huang Lab]   [HPEPDOCK]   [Help]   [Output example]  
Receptor Input using ONE of the following four options: [help]
Peptide(s) Input using ONE of the following four options for [help]

Advanced Options: Specify binding site, output, and docking parameters. (Optional)

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newSupports multiple-pepetide input, cyclic peptides, and nonstandard residues.

  1. Zhou P, Jin B, Li H, Huang SY. HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Res. 2018;46(W1):W443-W450.
  2. Tao H, Zhao X, Zhang K, Lin P, Huang SY. Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy. Bioinformatics. 2022;38(17):4109-4116.
  3. Tao H, Wu Q, Zhao X, Lin P, Huang SY. Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. J Cheminform. 2022;14(1):26.
  4. Tao H, Zhang Y, Huang SY. Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. J Chem Inf Model. 2020;60(4):2377-2387.
  5. Zhou P, Li B, Yan Y, Jin B, Wang L, Huang SY. Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. J Chem Inf Model. 2018;58(6):1292-1302.
  6. Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579.
  7. Huang SY, Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins. 2007;66:399-421.
If you submit protein sequences, please also cite:
  1. Remmert M, Biegert A, Hauser A, Soding 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. 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.
  5. 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: 2023-09-09
© Lab of Biophysics and Molecular Modeling, huanglab@hust.edu.cn