title: NLDB: a database for 3D protein-ligand interactions in enzymatic reactions.
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.
authors.affiliation: Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.|Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Saito-Asagi 7-6-8, Ibaraki-city, Osaka, 567-0085, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Murakami
authors.affiliation: Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Omori
authors.affiliation: Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan. kengo@ecei.tohoku.ac.jp.|Institute of Development, Aging and Cancer, Tohoku University, Seiryo-machi 4-1, Aoba-ku, Sendai, 980-8575, Japan. kengo@ecei.tohoku.ac.jp.|Tohoku Medical Megabank Organization, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8573, Japan. kengo@ecei.tohoku.ac.jp.
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008024:Ligands; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D008024:Ligands; D011506:Proteins
keywords: Database; Docking; Enzymatic reactions; Protein–ligand interactions; Variant residues