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This article is part of the supplement: Symposium of Computations in Bioinformatics and Bioscience (SCBB07)

Open Access Open Badges Research

Evolutionary conservation of DNA-contact residues in DNA-binding domains

Yao-Lin Chang1, Huai-Kuang Tsai2, Cheng-Yan Kao13*, Yung-Chian Chen4, Yuh-Jyh Hu5 and Jinn-Moon Yang467*

Author Affiliations

1 Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan

2 Institute of Information Science, Academia Sinica, Taipei 115, Taiwan

3 Institute for Information Industry, Taipei 106, Taiwan

4 Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan

5 Department of Computer Science, National Chiao Tung University, Hsinchu 30050, Taiwan

6 Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan

7 Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan

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BMC Bioinformatics 2008, 9(Suppl 6):S3  doi:10.1186/1471-2105-9-S6-S3

Published: 28 May 2008



DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues.


Our method achieves high precision and recall for 66 families of DNA-binding domains, with a false positive rate less than 5% for 250 non-DNA-binding proteins. In addition, experimental results show that our method is able to identify the different DNA-binding behaviors of proteins in the same SCOP family based on the use of evolutionary conservation of DNA-contact residues.


This study shows the conservation of DNA-contact residues in DNA-binding domains. We conclude that the members in the same subfamily bind DNA specifically and the members in different subfamilies often recognize different DNA targets. Additionally, we observe the co-evolution of DNA-contact residues and interacting DNA base-pairs.