標題: Prediction of Metal Ion-Binding Sites in Proteins Using the Fragment Transformation Method
作者: Lu, Chih-Hao
Lin, Yu-Feng
Lin, Jau-Ji
Yu, Chin-Sheng
生物資訊及系統生物研究所
Institude of Bioinformatics and Systems Biology
公開日期: 18-六月-2012
摘要: The structure of a protein determines its function and its interactions with other factors. Regions of proteins that interact with ligands, substrates, and/or other proteins, tend to be conserved both in sequence and structure, and the residues involved are usually in close spatial proximity. More than 70,000 protein structures are currently found in the Protein Data Bank, and approximately one-third contain metal ions essential for function. Identifying and characterizing metal ion-binding sites experimentally is time-consuming and costly. Many computational methods have been developed to identify metal ion-binding sites, and most use only sequence information. For the work reported herein, we developed a method that uses sequence and structural information to predict the residues in metal ion-binding sites. Six types of metal ion-binding templates-those involving Ca2+, Cu2+, Fe3+, Mg2+, Mn2+, and Zn2+-were constructed using the residues within 3.5 angstrom of the center of the metal ion. Using the fragment transformation method, we then compared known metal ion-binding sites with the templates to assess the accuracy of our method. Our method achieved an overall 94.6 % accuracy with a true positive rate of 60.5 % at a 5 % false positive rate and therefore constitutes a significant improvement in metal-binding site prediction.
URI: http://dx.doi.org/e39252
http://hdl.handle.net/11536/16476
ISSN: 1932-6203
DOI: e39252
期刊: PLOS ONE
Volume: 7
Issue: 6
結束頁: 
顯示於類別:期刊論文


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  1. 000305583300122.pdf