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Nucleic Acids Research 2006 34(Web Server issue):W124-W127; doi:10.1093/nar/gkl104
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Article

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition

Shandar Ahmad1,4, Hidetoshi Kono2,3, Marcos J. Araúzo-Bravo1 and Akinori Sarai1,*

1 Department of Bioscience and Bioinformatics, Kyushu Institute of Technology Iizuka 820 8502, Fukuoka, Japan 2 Computational Biology Group, Neutron Biology Research Center, Japan Atomic Energy Agency (JAEA) 8-1 Umemidai, Kizu-cho, Souraku-gun, Kyoto, 619-0215 Japan 3 PRESTO, Japan Science and Technology Agency 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan 4 Department of Biosciences, Jamia Millia Islamia University New Delhi-110025, India

*To whom correspondence should be addressed. Tel: 81 948 29 7811; Fax: 81 948 29 7841; Email: sarai{at}bse.kyutech.ac.jp

Received February 14, 2006. Revised February 24, 2006. Accepted March 8, 2006.

Protein–DNA interactions play a central role in regulatory processes at the genetic level. DNA-binding proteins recognize their targets by direct base–amino acid interactions and indirect conformational energy contribution from DNA deformations and elasticity. Knowledge-based approach based on the statistical analysis of protein–DNA complex structures has been successfully used to calculate interaction energies and specificities of direct and indirect readouts in protein–DNA recognition. Here, we have implemented the method as a webserver, which calculates direct and indirect readout energies and Z-scores, as a measure of specificity, using atomic coordinates of protein–DNA complexes. This server is freely available at http://gibk26.bse.kyutech.ac.jp/jouhou/readout/. The only input to this webserver is the Protein Data Bank (PDB) style coordinate data of atoms or the PDB code itself. The server returns total energy Z-scores, which estimate the degree of sequence specificity of the protein–DNA complex. This webserver is expected to be useful for estimating interaction energy and DNA conformation energy, and relative contributions to the specificity from direct and indirect readout. It may also be useful for checking the quality of protein–DNA complex structures, and for engineering proteins and target DNAs.


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