title: Predicting flavin and nicotinamide adenine dinucleotide-binding sites in proteins using the fragment transformation method.
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.
authors.affiliation: Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung 40402, Taiwan ; Graduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan.
authors.forename: Chih-Hao
authors.identifier: 0000-0002-8363-6244
authors.initials: CH
authors.lastname: Lu
authors.affiliation: Department of Information Engineering and Computer Science, Feng Chia University, Taichung 40724, Taiwan ; Master's Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, Taichung 40724, Taiwan.
authors.forename: Chin-Sheng
authors.identifier: 0000-0002-5205-1331
authors.initials: CS
authors.lastname: Yu
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan.
authors.forename: Yu-Feng
authors.initials: YF
authors.lastname: Lin
authors.affiliation: Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung 40402, Taiwan.
authors.forename: Jin-Yi
authors.initials: JY
authors.lastname: Chen
mesh_terms: D000596:Amino Acids; D001665:Binding Sites; D001671:Biochemistry / Q000379:methods*; D005182:Flavin-Adenine Dinucleotide / Q000378:metabolism*; D008958:Models, Molecular; D009243:NAD / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry*; D060388:Support Vector Machine
chemical_list: D000596:Amino Acids; D011506:Proteins; D009243:NAD; D005182:Flavin-Adenine Dinucleotide