2026-06-14T03:31:21Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/99132024-11-29T14:47:14Zcom_20.500.12105_2052com_20.500.12105_2051com_20.500.12105_2173col_20.500.12105_19609col_20.500.12105_19597
Repisalud
author
Maietta, Paolo
author
Gomez Lopez, Gonzalo
author
Carro, Angel
author
Pingilley, Benjamin J
author
Leon, Leticia G
author
Valencia, Alfonso
author
Tress, Michael
funder
Ministerio de Economía y Competitividad (España)
funder
Instituto de Salud Carlos III
funder
Unión Europea
2020-05-06T08:28:38Z
2020-05-06T08:28:38Z
2014-01
Nucleic Acids Res. 2014 Jan;42(Database issue):D267-72.
10.1093/nar/gkt1127
1362-4962
0305-1048
Nucleic acids research
24243844
http://hdl.handle.net/20.500.12105/9913
FireDB (http://firedb.bioinfo.cnio.es) is a curated inventory of catalytic and biologically relevant small ligand-binding residues culled from the protein structures in the Protein Data Bank. Here we present the important new additions since the publication of FireDB in 2007. The database now contains an extensive list of manually curated biologically relevant compounds. Biologically relevant compounds are informative because of their role in protein function, but they are only a small fraction of the entire ligand set. For the remaining ligands, the FireDB provides cross-references to the annotations from publicly available biological, chemical and pharmacological compound databases. FireDB now has external references for 95% of contacting small ligands, making FireDB a more complete database and providing the scientific community with easy access to the pharmacological annotations of PDB ligands. In addition to the manual curation of ligands, FireDB also provides insights into the biological relevance of individual binding sites. Here, biological relevance is calculated from the multiple sequence alignments of related binding sites that are generated from all-against-all comparison of each FireDB binding site. The database can be accessed by RESTful web services and is available for download via MySQL.
eng
FireDB: a compendium of biological and pharmacologically relevant ligands
research article
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URL
https://repisalud.isciii.es/bitstreams/e53b9425-28f6-46f4-b725-cf9f6f9be30e/download
File
MD5
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application/pdf
FireDBACompendiumOf_2014.pdf
URL
https://repisalud.isciii.es/bitstreams/102f48fe-ebc3-48c9-90f5-efcec9778d3c/download
File
MD5
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text/plain
FireDBACompendiumOf_2014.pdf.txt