ArticleNucleic acids research2014
FireDB: a compendium of biological and pharmacologically relevant ligands.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- FURNA: A database for functional annotations of RNA structures.PLoS biology · 2024Article
- Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions.Genomics, proteomics & bioinformatics · 2024Article
- BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic acids research · 2024Article
- UniProt: the Universal Protein Knowledgebase in 2023.Nucleic acids research · 2023Article
- Annotation of biologically relevant ligands in UniProtKB using ChEBI.Bioinformatics (Oxford, England) · 2023Article
- Article
- Delineating the RAS Conformational Landscape.Cancer research · 2022Article
- The properties of human disease mutations at protein interfaces.PLoS computational biology · 2022Article
- The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.Bioinformatics (Oxford, England) · 2019Article
- Protein ligand-specific binding residue predictions by an ensemble classifier.BMC bioinformatics · 2016Article
- Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.PloS one · 2016Article
- Practical Approaches for Mining Frequent Patterns in Molecular Datasets.Bioinformatics and biology insights · 2016Review
- I-TASSER server: new development for protein structure and function predictions.Nucleic acids research · 2015Article
- sc-PDB: a 3D-database of ligandable binding sites--10 years on.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
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.
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