Elucidation of Protein Structural and Pharmacophore Features Based on Sequence Clustering by Common Neighbor Comparisons

INTRODUCTION. Genome sequencing projects have dramatically increased our understanding of the pathways and proteins involved in biological systems. The NAD(P)-utilizing family of enzymes is one of the most important gene families representing 15% of all known enzyme functions. We have performed a complete characterization of this gene family on a sequence, structural, and NAD(P)-pharmacophore level. Genome-wide analysis was performed to gain a complete understanding of the structures and functional importance of NAD(P)-utilizing enzymes in 17 different genomes.