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Protocols

FireDB specifications

Information


Unique identifier OMICS_03007
Name FireDB
Restrictions to use None
Maintained Yes

Publication for FireDB

FireDB citations

 (7)
call_split

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues

2018
BMC Bioinformatics
PMCID: 5827975
PMID: 29482506
DOI: 10.1186/s12859-018-2084-7
call_split See protocol

[…] ce identity ≥25%, aligned region ≥50%). With these criteria, we found a homolog of known structure for 67 out of the 121 proteins. We retrieved the binding sites annotated for these structures in the FireDB database []. For a given set of predicted functional residues in a given family (SDPs and fully conserved sites) we calculated their average distance to the annotated binding sites in the homol […]

library_books

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

2013
Nucleic Acids Res
PMCID: 3965027
PMID: 24316579
DOI: 10.1093/nar/gkt1282

[…] e the DNA binding specificities of closely related TFs (). The protein database section includes annual updates on UniProt and KEGG, as well as updates of such popular databases as Pfam, eggNOG, ELM, FireDB, SEED, SIMAP and Transporter protein Classification DataBase (TCDB). Two new databases, HRaP and RepeatsDB, collect information on protein repeats, the former at the sequence level (runs of the […]

library_books

Insight into the Assembly Properties and Functional Organisation of the Magnetotactic Bacterial Actin like Homolog, MamK

2012
PLoS One
PMCID: 3346761
PMID: 22586444
DOI: 10.1371/journal.pone.0034189

[…] ns in order to detect remote homologies beyond the reach of some other sequence comparison methods. The sequence identity between the two proteins was 22%. We further used the server Firestar (http://firedb.bioinfo.cnio.es/Php/FireStar.php), to predict functional residues for the sequence of MamK and also I-TASSER server (http://zhang.bioinformatics.ku.edu/I-TASSER) to predict the binding site res […]

library_books

Identification of binding pockets in protein structures using a knowledge based potential derived from local structural similarities

2012
BMC Bioinformatics
PMCID: 3434446
PMID: 22536963
DOI: 10.1186/1471-2105-13-S4-S17

[…] and uses the center of mass of the ligands to identify putative binding sites. The predicted sites are then ranked according to the number of templates sharing the binding pocket. Firestar integrates FireDB, a database of annotated functional residues, with a sequence alignment tool in order to enable the comparison of binding residues across homologous proteins. When possible the information of w […]

library_books

firestar—advances in the prediction of functionally important residues

2011
Nucleic Acids Res
PMCID: 3125799
PMID: 21672959
DOI: 10.1093/nar/gkr437

[…] ded. The sequence is extracted from the 3D structure.PSI-BLAST () profiles are generated for the sequences from a locally generated 70% redundant database. The profiles are used to search against the FireDB template database.Users may specify the BLAST e-value cut-off for the final search of the FireDB templates; note that the default e-value is intentionally high as functional information will be […]

library_books

firestar—prediction of functionally important residues using structural templates and alignment reliability

2007
Nucleic Acids Res
PMCID: 1933227
PMID: 17584799
DOI: 10.1093/nar/gkm297

[…] es or coordinates in PDB format. Target sequences are subjected to standard PSI-BLAST searches. Profiles are generated with an nrdb90 database from the EBI () and the final search is made against the FireDB consensus sequence database. Functional residues mapped onto the resulting alignments and the reliability of each position in the alignment is evaluated with SQUARE. The residue scores from SQU […]

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FireDB institution(s)
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain; Spanish National Bioinformatics Institute (INB-ISCIII), Spain

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