MPRDock Server
[Huang Lab]   [MPRDock]   [Help]   [Output example]  
 Input Receptor Protein (Single chain only) using ONE of the following four options: [help]
 Input Ligand RNA/DNA using ONE of the following two options: [help]
 Docking Parameter:
    Maximum number of protein models used for ensemble docking [0-10] : 
    Enter your email:     
    Enter your jobname:

Option I: Specify the residues of the binding site.


  1. He J, Tao H, Huang SY. Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinformatics. 2019 May 14. pii: btz388. doi: 10.1093/bioinformatics/btz388.
  2. 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.
  3. 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.
  4. 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.
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. 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,