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Bioinformatics Advance Access published online on January 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg432
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received February 26, 2003
Revised May 26, 2003
Accepted July 26, 2003

Article

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

Shandar Ahmad 1*, M. Michael Gromiha 2, Akinori Sarai 1

1 Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka, Japan
2 Computational Biology Research Center (CBRC), AIST, 2-41-6, Aomi, Koto-ku, Tokyo 135 0064, Japan

* To whom correspondence should be addressed. E-mail: shandar{at}bse.kutech.ac.jp.


  Abstract

Motivation:

Though vitally important to cell function, the mechanism of protein-DNA binding has not yet been completely understood. We therefore analyzed the relationship between DNA-binding and protein sequence composition, solvent accessibility and secondary structure. Using non-redundant databases of transcription factors and Protein-DNA complexes, neural network models were developed to utilize the information present in this relationship to predict DNA-binding proteins and their binding residues.

Results:

Sequence composition was found to provide sufficient information to predict the probability of its binding to DNA with nearly 69% sensitivity at 64% accuracy for the considered proteins; sequence neighborhood and solvent accessibility information were sufficient to make binding site predictions with 40% sensitivity at 79% accuracy. Detailed analysis of binding residues shows that some three- and five-residue segments frequently bind to DNA and that solvent accessibility plays a major role in binding. Although, binding behavior was not associated with any particular secondary structure, there were interesting exceptions at the residue level. Over-representation of some residues in the binding sites was largely lost at the total sequence level, but a different kind of compositional preference was observed in DNA-binding proteins.

Availability: Online predictions of DNA binding proteins and binding sites are available at http://www.netasa.org/dbs-pred/


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