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 |
顯示於類別: | 會議論文 |