Connecting a DNA-binding protein with its binding sites

DBD2BS uses the structure of DNA binding domains (DBDs) to predict the corresponding binding sites on DNA. Queries can be specified by a PDB ID or the coordinates of a DNA-binding protein in PDB format. Users do not have to mark the DBD, which will be identified by DBD2BS automatically. DBD2BS is the first web server that can predict binding sites from protein unbound structures, in addition to using native protein-DNA complexes directly. For the users’ convenience, DBD2BS currently maintains a list of 2,176 protein-DNA complexes and 3,135 unbound structures of DNA-binding proteins collected from PDB.

Query examples

  1. A structure of mouse transcription factor, Zif268. You could use it as input or see a sample result for it.
  2. A catabolite gene activator of E. coli. This example demonstrates how to use DBD2BS with a protein-DNA complex as the query. You could use it as input or see a sample result for it. (see tutorial)
  3. A amino acid biosynthesis regulatory protein of yeast. You could use it as input by its PDB ID or use it as input by a coordinate file or see a sample result for it. (see tutorial)

Query with a protein structure

    Only the protein chain (the first protein chain if there are many) in the input will be extracted and superimposed into our templates.
  • (e.g. 1AAY:A)
  • Protein structure (coordinates in PDB format)

Query with a protein-DNA complex

You can input a protein-DNA complex produced by yourself, rather than asking the DBD2BS to perform the alignment-based template search and complex production.
  • (e.g. 1AAY)


  1. Chen, C.-Y., Chien, T.-Y., Lin, C.-K., Lin, C.-W., Weng, Y.-Z. and Chang, D.T.-H. (2012) Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures. PLoS ONE, 7, e30446.