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BioMed Research International
Volume 2015, Article ID 402536, 13 pages
http://dx.doi.org/10.1155/2015/402536
Research Article

Predicting Flavin and Nicotinamide Adenine Dinucleotide-Binding Sites in Proteins Using the Fragment Transformation Method

1Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung 40402, Taiwan
2Graduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan
3Department of Information Engineering and Computer Science, Feng Chia University, Taichung 40724, Taiwan
4Master’s Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, Taichung 40724, Taiwan
5Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan

Received 16 June 2014; Accepted 21 July 2014

Academic Editor: Hao-Teng Chang

Copyright © 2015 Chih-Hao Lu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We developed a computational method to identify NAD- and FAD-binding sites in proteins. First, we extracted from the Protein Data Bank structures of proteins that bind to at least one of these ligands. NAD-/FAD-binding residue templates were then constructed by identifying binding residues through the ligand-binding database BioLiP. The fragment transformation method was used to identify structures within query proteins that resembled the ligand-binding templates. By comparing residue types and their relative spatial positions, potential binding sites were identified and a ligand-binding potential for each residue was calculated. Setting the false positive rate at 5%, our method predicted NAD- and FAD-binding sites at true positive rates of 67.1% and 68.4%, respectively. Our method provides excellent results for identifying FAD- and NAD-binding sites in proteins, and the most important is that the requirement of conservation of residue types and local structures in the FAD- and NAD-binding sites can be verified.