標題: Evolutionary conservation of DNA-contact residues in DNA-binding domains
作者: Chang, Yao-Lin
Tsai, Huai-Kuang
Kao, Cheng-Yan
Chen, Yung-Chian
Hu, Yuh-Jyh
Yang, Jinn-Moon
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 2008
摘要: Background: 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. Results: 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. Conclusion: 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.
URI: http://hdl.handle.net/11536/9777
http://dx.doi.org/10.1186/1471-2105-9-S6-S3
ISSN: 1471-2105
DOI: 10.1186/1471-2105-9-S6-S3
期刊: BMC BIOINFORMATICS
Volume: 9
Appears in Collections:Conferences Paper


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