metaDBSite: a meta web server for protein DNA-binding sites prediction based on protein sequence!

Based Servers:

We use the prediction results from the following prediction servers to build up our meta prediction method:

  • BindN
  • BindN-RF
  • DNABindR
  • DP-Bind
  • We thank the authors of DISIS, DNABindR, BindN, BindN-rf, DP-Bind and DBS-PRED for making their tools available. If you have your own tool for identification of DNA-binding sites and would like to be included into our metaDBSite approach, please send us an e-mail and we will be very happy about that.

    Notice: Benchmark dataset: the PDNA-316 dataset used in the metaDBSite manuscript is redundant. Now we clean up the redundancy in it and the new non-redundant data-set is called PDNA-232 and can be downloaded here. We apologize for this redundancy. Please refer to the new PDNA-232 data-set for your purpose.
    Update Benchmark dataset: We also generate the new benchmark dataset for protein-DNA binding site prediction from the PDB in March 2013 using the same procedure. The new data-set is called PDNA-422 and can be downloaded here.

    1. Please input your e-mail address here (for e-mail sending about the result, optional: help

    2. Please give your sequence a name here (for annotation of the result only, optional): help

    3. Please paste your protein sequence here: help
    • protein sequence must in fasta format or sequence only
    • all residues must be in one-letter code
    • any number of white spaces or break lines are allowed in sequence
    • please set the code of non-standard residues to 'X'



    - Before using metaDBSite, please read our help page.
    - The algorithm of metaDBSite is illustrated here.
    - It might take up to 10 minutes to predict the DNA-binding sites depending on the length of your input protein sequence and the status of other prediction servers. Please be patient!




    If this server is useful for your work, please cite:

    JingNa Si, Zengming Zhang, Biaoyang Lin, Michael Schroeder, Bingding Huang (2011), metaDBSite: a meta approach to improve protein DNA-binding site prediction , BMC Systems Biology, 5:S7 link.

    Contact us

    Bingding Huang(Project leader), Email:
    Zengming Zhang, Email:
    Jingna Si, Email:

    Report Bugs

    If you find some bugs of this server, please help us improve it by reporting bugs to <Zengming Zhang>, any help from you will be greatly appreciated!


    Funding from MOST China (grant no: 2008DFA11320) and EU 7th Framework Marie Curie Actions IRSES project (grant no: 247097) is acknowledged!