ArticleJournal of structural and functional genomics2016
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions.
Article in Journal of structural and functional genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Augmented BindingNet dataset for enhanced ligand binding pose predictions using deep learning.npj drug discovery · 2025Article
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- VaProS: a database-integration approach for protein/genome information retrieval.Journal of structural and functional genomics · 2016Article
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3 authors.
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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.
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