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Receptor Input using ONE of the following four options: [help]
Peptide Input using ONE of the following four options: [help]

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

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  1. Zhou P, Jin B, Li H, Huang S-Y.* HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Research, doi: 10.1093/nar/gky357, 2018.
  2. Zhou P, Li B, Yan Y, Jin B, Wang L, Huang S-Y.* Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. Journal of Chemical Information and Modeling, doi: 10.1021/acs.jcim.8b00142, 2018.
  3. Yan Y, Zhang D, Huang S-Y.* Efficient conformational ensemble generation of protein-bound peptides. J Cheminform. 2017;9(1):59.
  4. Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579.
  5. 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 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: 2021-11-13
© Lab of Biophysics and Molecular Modeling, huanglab@hust.edu.cn