[Huang Lab]   [HNADOCK]   [Help]   [Output example]  
First Nucleic Acid Molecule using ONE of the following three options: [help]
Second Nucleic Acid Molecule using ONE of the following three options: [help]
Modeling Options:
    RNA secondary structure prediction method :    [help]
    RNA-RNA interaction prediction method :    [help]
    Refine the top 10 complex models :    [help]
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Option I: Specify the residues of the binding site.


  1. He J, Wang J, Tao H, Xiao Y, Huang SY. HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. Nucleic Acids Res. 2019 May 22. pii: gkz412. doi: 10.1093/nar/gkz412.
  2. Huang SY, Zou X. MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins, 78: 3096-103, 2010.
  3. Zhao Y, Huang Y, Gong Z, Wang Y, Man J, Xiao Y. Automated and fast building of three-dimensional RNA structures. Sci Rep, 2: 734, 2012.
  4. 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, 85: 497-512, 2017.
  5. Wang J, Mao K, Zhao Y, Zeng C, Xiang J, Zhang Y, Xiao Y. Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis. Nucleic Acids Res, 45: 6299-6309, 2017.
  6. Yan Y, Wen Z, Zhang D, Huang S-Y. Determination of an effective scoring function for RNA–RNA interactions with a physics-based double-iterative method. Nucleic Acids Res, 46: e56, 2018.
  7. Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlic A, Rose PW. NGL viewer: web-based molecular graphics for large complexes. Bioinformatics, 34: 3755-3758, 2018.
The PDB database is updated monthly. Current version: 2019-08-24
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