TFmodeller: comparative modelling of protein-DNA complexes

Bioinformatics. 2007 Jul 1;23(13):1694-6. doi: 10.1093/bioinformatics/btm148. Epub 2007 Apr 25.


Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at atomic scale, but the molecular details of many others remain to be discovered. TFmodeller exploits the current knowledge about protein-DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology. Results are emailed to the user and include an evolutionary contact matrix, a schematic representation of the putative binding interface and atomic coordinates of the modelled complex. The library of complexes used by TFmodeller is updated on a weekly basis and is available for download.

Availability: TFmodeller and its web service interface are free for academic users at

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Binding Sites
  • Computer Simulation
  • DNA / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Databases, Protein
  • Models, Chemical*
  • Protein Binding
  • Sequence Analysis, Protein / methods*


  • DNA-Binding Proteins
  • DNA