Abstract
NLDB (Natural Ligand DataBase; URL: http://nldb.hgc.jp) is a database of automatically collected and predicted 3D protein–ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Structural information about these reactions is important for studying the molecular functions of enzymes, however a large number of the 3D interactions are still unknown. Therefore, in order to complement such missing information, we predicted protein–ligand complex structures, and constructed a database of the 3D interactions in reactions. NLDB provides three different types of data resources; the natural complexes are experimentally determined protein–ligand complex structures in PDB, the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations. In addition, NLDB shows the known polymorphisms found in human genome on protein structures. The database has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs. NLDB will be a valuable resource for experimental biologists studying protein–ligand interactions in specific reactions, and for theoretical researchers wishing to undertake more precise simulations of interactions.
Highlights
Protein–ligand interactions play key roles in almost all biological processes, ranging from enzyme catalysis to signal transduction
NLDB (Natural Ligand DataBase; URL: http:// nldb.hgc.jp) is a database of automatically collected and predicted 3D protein–ligand interactions for the enzymatic reactions of metabolic pathways registered in Kyoto Encyclopedia of Genes and Genomes (KEGG)
NLDB provides three different types of data resources; the natural complexes are experimentally determined protein– ligand complex structures in Protein Data Bank (PDB), the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations
Summary
Protein–ligand interactions play key roles in almost all biological processes, ranging from enzyme catalysis to signal transduction. The large-scale structural information for protein–ligand interactions is currently available in the Protein Data Bank (PDB; [2]), and has contributed to the physicochemical analyses of their interactions. This wealth of information is not still enough to physicochemically explain all of the enzymatic reactions with the enzymes that are important potential drug targets [6]. Catalyzing a reaction of interest is available in PDB, its structures in a complex with substrates or products in the reaction are not always experimentally determined In such cases, detailed information about the 3D interaction characteristics in natural ligands may not be obtained. NLDB is a unique, up-to-date database that collects 3D protein–ligand interactions from known structures and automatically predicts complex structures that were previously unknown
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