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FireDB


NAR Molecular Biology Database Collection entry number 986
Tress, Michael; Maietta, Paolo; Lopez, Gonzalo; Carro, Angel; Leon, Leticia; Pingilley, Benjamin; Valencia, Alfonso
Spanish National Cancer Research Center, Structural and Computational Biology Program, C/ Melchor Fern√°ndez Almagro, 3, E-28029 Madrid, Spain
Contact mtress@cnio.es

Database Description

FireDB is a fully automated search system for structures in the Protein Data Bank(PDB), that contain annotations of residues participating in a functional site. The sources of functional residues are protein-ligand atom contacts and the Catalytic Site Atlas.
The whole PDB was clustered at 97% sequence identity and every chain mapped onto a consensus (Master sequence) from the cluster, so that important positions can be mapped and binding sites collapsed into the master sequence. Comparison of binding sites within a cluster of sequences gives an idea of the flexibility of those regions and the capability they have to bind different ligand analogs. Another utility is the biological relevance assesment of small molecule binding sites found in the PDB structures.
The Database can be accessed by PDB codes,Uniprot primary accession numbers or keywords as well as small molecule ligands. Molecular visualzationis is also available when navigating across FireDB.

Acknowledgements

1. An European Network for Integrated Genome Annotation. Ref. U.E. : LSHG-CT-2003-503265.
2. In-silico prediction of gene function. Ref. U.E. : LSHG-CT-2004-503567.
3. Especificidad funcional en proteínas. Ref. MEC : BIO2004-00875.


Go to the abstract in the NAR 2014 Database Issue.
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