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• W2517767579 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." @default.
• W2517767579 created "2016-09-16" @default.
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• W2517767579 date "2016-08-16" @default.
• W2517767579 modified "2023-09-23" @default.
• W2517767579 title "NLDB: a database for 3D protein–ligand interactions in enzymatic reactions" @default.
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• W2517767579 doi "https://doi.org/10.1007/s10969-016-9206-0" @default.
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