LIGAND: database of chemical compounds and reactions in biological pathways

By Susumu Goto, Yasushi Okuno, Masahiro Hattori, T. Nishioka, Minoru Kanehisa. Nucleic Acids Res., 2002

309 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4c2a5b1764e56e494c83c07deedc96957f8014d6

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Citations in the corpus

The Edinburgh human metabolic network reconstruction and its functional analysis (2007, methodology): “We ﬁrst used the KEGG ligand database to generate the reaction list, because it is one of the most complete metabolic reaction databases including more than 7000 reactions (Goto et al , 2002).”
Using the KEGG Database Resource (2005, background): “KEGG LIGAND is a composite database name for chemical information in KEGG (Goto et al., 2002; Kanehisa et al., 2004, 2006).”
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. (2003, methodology): “We have used chemical compound data in the COMPOUND section of the KEGG/LIGAND database (version 20.0 + update 2002/03/26), 32,33 which is maintained in the ISIS/Oracle database system.”
Plant metabolomics: large-scale phytochemistry in the functional genomics era. (2003, methodology): “KEGG also includes the LIGAND (Goto et al., 2002) database of molecules and reactions.”
Computational Methods in Drug Discovery (2014, background): “ROSETTALIGAND was used by Kaufmann et al. (2009) to predict the binding mode of serotonin with serotonin transporters.”
The KEGG databases at GenomeNet (2002, background): “As described elsewhere in this issue (13), a web-based chemical structure search is now available for the COMPOUND and REACTION sections, which are stored in the ISIS system.”
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms (2003, methodology): “Our reaction database is based on the KEGG LIGAND database (Goto et al., 1998, 2002).”
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) (2003, background): “Sequence annotations A list of reactions and associated enzymes that could connect the dead ends with the rest of the network was gathered from LIGAND (Database of Chemical Compounds and Reactions in Biological Pathways [13]).”
Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles (2009, methodology): “Here, we used compounds available from the Kyoto Encyclopedia of Gene and Genomics (KEGG) database (Goto et al. 2002) and the Human Metabolome Database (HMDB) (Wishart et al. 2007) as candidates.”
GLIDA: GPCR-ligand database for chemical genomic drug discovery (2005, background): “PubChem (http://pubchem.ncbi. nlm.nih.gov/) (6), KEGG/LIGAND (http://www.genome.jp/ kegg/ligand.html) ( 7 ) and ChEBI (http://www.ebi.ac.uk/ chebi/) (8) have been developed as databases related to chemical genomics.”
VANTED: A system for advanced data analysis and visualization in the context of biological networks (2006, methodology): “The mapping procedure also considers any synonym or identifier defined in the KEGG Ligand database [29] or in the SIB (Swiss Institute of Bioinformatics) Enzyme nomenclature database [30].”
Chemical space and biology (2004, background): “The simplest living organisms can function with just a few hundred different types of such molecule, and fewer than 100 account for nearly the entire molecular poo”
The KEGG resource for deciphering the genome (2004, methodology): “The COMPOUND/REACTION databases are being moved from the ISIS system ( 5 ) to the in-house-developed relational database system, in order to integrate with the GLYCAN database.”