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This article is part of the supplement: Selected articles from the 4th International Conference on Computational Systems Biology (ISB 2010)

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MetaDBSite: a meta approach to improve protein DNA-binding sites prediction

Jingna Si13, Zengming Zhang1, Biaoyang Lin1, Michael Schroeder2 and Bingding Huang12*

Author Affiliations

1 Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, Kaixuan Road 268, 310029, Hangzhou, China

2 Bioinformatics Group, Biotechnology Center, Technical University of Dresden, Tatzbergstr 47, 01307, Dresden, Germany

3 College of Biological Sciences, China Agricultural University, 100193, Beijing, China

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BMC Systems Biology 2011, 5(Suppl 1):S7  doi:10.1186/1752-0509-5-S1-S7

Published: 20 June 2011



Protein-DNA interactions play an important role in many fundamental biological activities such as DNA replication, transcription and repair. Identification of amino acid residues involved in DNA binding site is critical for understanding of the mechanism of gene regulations. In the last decade, there have been a number of computational approaches developed to predict protein-DNA binding sites based on protein sequence and/or structural information.


In this article, we present metaDBSite, a meta web server to predict DNA-binding residues for DNA-binding proteins. MetaDBSite integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, BindN-rf, DP-Bind and DBS-PRED and it solely uses sequence information of proteins. A large dataset of DNA-binding proteins is constructed from the Protein Data Bank and it serves as a gold-standard benchmark to evaluate the metaDBSite approach and the other six predictors.


The comparison results show that metaDBSite outperforms single individual approach. We believe that metaDBSite will become a useful and integrative tool for protein DNA-binding residues prediction. The MetaDBSite web-server is freely available at webcite and webcite.