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

Abstract EN

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.