Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(4) © Oxford University Press 2004; all rights reserved.
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
1 Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Fukuoka, Iizuka 820 8502, Japan, 2 Department of Biosciences, Jamia Mila Islamia, New Delhi 110025, India and 3 Computational Biology Research Center (CBRC), AIST, 2-41-6, Aomi, Koto-ku, Tokyo 135 0064, Japan
Received on February 26, 2003
; revised on May 26, 2003
; accepted on July 26, 2003
Advance Access Publication January 22, 2004
Motivation: Though vitally important to cell function, the mechanism of protein–DNA binding has not yet been completely understood. We therefore analysed 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 neighbourhood 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 behaviour 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/
Contact: shandar{at}bse.kyutech.ac.jp
* To whom correspondence should be addressed at present address: Department of Biochemical Science, Engineering, Kyushu Institute of Technology, Fukuoka, Iizuka 820 8502, Japan.
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