FireDB
fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.
Description
More detailed information about this field from each metasource.
fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.
metasource: Fairsharing.orgversion: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://firedb.bioinfo.cnio.es/Webpage
More detailed information about this field from each metasource.
http://firedb.bioinfo.cnio.es/
metasource: Fairsharing.orgversion: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
FireDB--a database of functionally important residues from proteins of known structure
PMID: 17132832
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
FireDB: a compendium of biological and pharmacologically relevant ligands
PMID: 24243844
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkt1127
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
FireDB--a database of functionally important residues from proteins of known structure
PMID: 17132832
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
FireDB: a compendium of biological and pharmacologically relevant ligands
PMID: 24243844
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkt1127
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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FireDB--a database of functionally important residues from proteins of known structure
PubMed citations: 34.
34 articles citing: FireDB--a database of functionally important residues from proteins of known structure
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. PMID:35524575
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3. PMID:34432238
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. PMID:29482506
KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily. PMID:27357839
Impact of germline and somatic missense variations on drug binding sites. PMID:26810135
Computer analysis of protein functional sites projection on exon structure of genes in Metazoa. PMID:26693737
A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets. PMID:26561508
In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces. PMID:25393408
Assessment of ligand binding site predictions in CASP10. PMID:24339001
wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases. PMID:24289158
Exploring the composition of protein-ligand binding sites on a large scale. PMID:24277997
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
APPRIS: annotation of principal and alternative splice isoforms. PMID:23161672
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. PMID:23087378
Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. PMID:23055974
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. PMID:22839973
Prioritization of pathogenic mutations in the protein kinase superfamily. PMID:22759651
Bioinformatics and variability in drug response: a protein structural perspective. PMID:22552919
Real value prediction of protein folding rate change upon point mutation. PMID:22426539
Characterization of pathogenic germline mutations in human protein kinases. PMID:21992016
The Proteome Folding Project: proteome-scale prediction of structure and function. PMID:21824995
firestar--advances in the prediction of functionally important residues. PMID:21672959
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. PMID:21575183
Structure-based identification of catalytic residues. PMID:21491495
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. PMID:21459847
Predicting conserved protein motifs with Sub-HMMs. PMID:20420695
FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PMID:20305778
Protein interactions and ligand binding: from protein subfamilies to functional specificity. PMID:20133844
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
PepX: a structural database of non-redundant protein-peptide complexes. PMID:19880386
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. PMID:17933762
firestar--prediction of functionally important residues using structural templates and alignment reliability. PMID:17584799 -
FireDB: a compendium of biological and pharmacologically relevant ligands
PubMed citations: 10.
10 articles citing: FireDB: a compendium of biological and pharmacologically relevant ligands
CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome. PMID:35883523
Delineating the RAS Conformational Landscape. PMID:35536216
3DLigandSite: structure-based prediction of protein-ligand binding sites. PMID:35412635
The properties of human disease mutations at protein interfaces. PMID:35120134
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis. PMID:29947739
Protein ligand-specific binding residue predictions by an ensemble classifier. PMID:27855637
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PMID:27467773
Practical Approaches for Mining Frequent Patterns in Molecular Datasets. PMID:27168722
I-TASSER server: new development for protein structure and function predictions. PMID:25883148
sc-PDB: a 3D-database of ligandable binding sites--10 years on. PMID:25300483 - http://dx.doi.org/10.1093/nar/gkt1127
Tags:
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: FireDB; FireDB; DOI: https://doi.org/10.25504/FAIRsharing.5125qd; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein protein structure protein sequence protein sequence motifs and active sites
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