Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
NCBI Gene - NCBI Gene United States 1802unstable47.13
UniProt - The Universal Protein Resource United Kingdom 13605unstable835.74
InterPro - Protein sequence analysis & classification United Kingdom 5033alive279.61
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive56.84
OMA - The Orthologous Matrix project United Kingdom 153unstable13.99
COG - Clusters of Orthologous Genes United States 11125unstable185.42
MBGD - Microbial Genome Database Japan 279alive18.23
MobiDB - A Database of Protein Disorder and Mobility Annotations Italy 80alive13.20
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable2.40
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive3.96
PTMcode Germany 56alive11.20
ProteomeScout United States 0unstable0.00
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable24.62
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive28.05
Ensembl - Ensembl United Kingdom 12662alive783.46
DDMGD - database of diseases associated gene methylation in different species Saudi Arabia 2unstable0.45
diArk - Database for Eukaryotic Genome Research Germany 16unstable1.18
uORFdb - upstream open reading frames database Germany 22unstable4.68
Pfam - Protein Families Database United Kingdom 19906alive947.90
ELM - The Eukaryotic Linear Motif Resource Germany 325unstable8.13
pE-DB - Protein Ensemble Database Belgium 55unstable12.93
EKPD - Database of Eukaryotic Protein Kinases China 12alive3.00
DEG - Database of Essential Genes China 573alive40.93
SILVA - High quality ribosomal RNA databases Germany 3927unstable82.11
RefSeq - Reference Sequence Database United States 6794unstable132.11
PhylomeDB - Phylome DataBase Spain 241alive24.10
Dfam - Dfam United States 58unstable8.93
UCNEbase - A database of ultraconserved non-coding elements and genomic regulatiory blocks Switzerland 20unstable3.16
GeneTack database - GeneTack database United States 6unstable0.26
PROSITE - Database of protein domains, families and functional sites Switzerland 8754unstable246.41
KEGG OC - KEGG Ortholog Cluster Japan 37alive7.40
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive170.80
PeroxiBase France 333alive27.75
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive4.40
ZiFDB - Zinc Finger Database United States 73dead0.00
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive35.14
PR2 - Protist Ribosomal Reference Database France 80alive16.00
metaMicrobesOnline - Phylogenomic Analysis of Microbial Communities United States 5alive0.99
GEO - Gene Expression Omnibus United States 9384unstable205.27
PRIDE - PRoteomics IDEntifications United Kingdom 846unstable108.29
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.56
GeneDB - GeneDB United Kingdom 92alive15.18
ProtoNet Israel 187alive12.34
Polbase - Polymerase Database United States 8unstable0.25
ProRepeat Netherlands 10unstable0.27
PASS2 - Protein Alignments organised as Structural Superfamilies India 70alive4.38
Pocketome United States 54unstable8.01
ProtChemSI - protein-chemical structural interactions Germany 9alive1.49
PSCDB - Protein Structural Change DataBase Japan 35alive5.00
GOLD - Genomes On Line Database United States 1646unstable26.06
UniPathway - UniPathway Switzerland 54unstable6.84
WikiPathways - WikiPathways Netherlands 228unstable17.10
RNAMDB - RNA Modification Database United States 1297unstable38.37
Phospho.ELM - A database of experimentally verified phosphorylation sites in eukaryotic proteins Germany 580unstable6.63
Phospho3D Spain 62alive5.52
PRIDB - Protein-RNA Interface Database United States 49unstable6.51
PREX - PeroxiRedoxin classification indEX United States 47alive6.71
VKCDB - voltage-gated potassium channels databse Canada 34alive2.43
PCDB - A database of protein conformational diversity Argentina 18alive2.55
PCDDB - Protein Circular Dichroism Data Bank United Kingdom 91alive7.58
PRO - Protein Ontology United States 163unstable17.93
PhEVER - phylogenetic exploration of virues' evolutionary relationships France 4unstable0.06
Pathway Commons - Search and visualize public biological pathway information United States 395alive56.43
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.43
ProtCID - Protein Common Interfaces Database United States 44alive6.22
The Autophagy Database Japan 25dead0.00
PROMISCUOUS Germany 109alive15.57
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.63
PDBWiki Germany 24alive3.00
GOOD - Gene-Oriented Ortholog Database Taiwan 3unstable0.32
Histone Database - Histone Database United States 19unstable0.52
PRINTS - A compendium of protein fingerprints United Kingdom 42alive6.72
PMP - Protein Model Portal Switzerland 43unstable5.85
piRBase - piRNA database China 6unstable1.41
PolyprOnline France 2unstable0.41
PTM-SD - Post Translational Modification Structural Database France 6alive1.49
PLIC - Protein-Ligand Interaction Clusters India 3alive0.74
PathLocdb - Pathway Localization Database China 10unstable0.23
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
RedoxDB - protein oxidative modification database Hong Kong SAR China 25alive4.13
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.74
UniCarb-DB - UniCarb-DB Australia 65dead0.00
DeOri - Database of Eukaryotic DNA Replication Origins China 12unstable1.60
TGI - TIGR Gene Index database United States 214alive16.46
UTRdb - UTRdb Italy 644unstable33.63
PDBSITE Russian Federation 92alive7.01
PRECISE - Predicted and Consensus Interaction Sites in Enzymes United States 16dead0.00
ProDom France 251alive19.31
PDB-Ligand Korea Rep. 58unstable1.96
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343unstable22.95
PFD - Protein Folding Database Australia 30unstable0.95
PartiGeneDB - A Database of Partial Genomes Canada 12unstable0.83
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive29.84
Recode-2 Ireland 35alive4.29
Polymorphix France 23unstable0.18
IRESite - Internal Ribosome Entry Site Czech Republic 126unstable9.97
ITS2 Database - Internal Transcribed Spacer 2 Database Germany 366alive30.50
PGD - Protein Geometry Database United States 19unstable1.33
PTGL - Protein Topology Graph Library Germany 10dead0.00
PNU - Protein Naming Utility United States 6unstable0.55
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60unstable5.93
Peptidome United States 30dead0.00
PSI-MR - Protein Structure Initiative Material Repository United States 105alive12.99
PeroxisomeDB - PEROXISOME database Spain 61alive7.55
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable231.15
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.47
ProTherm - Thermodynamic Database for Proteins and Mutants Japan 618dead0.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable11.82
PAZAR - A public database of transcription factor and regulatory sequence annotation Canada 65unstable6.21
GtRNAdb - Genomic tRNA Database United States 378alive41.58
PseudoBase++ - An extension of PseudoBase United States 38alive4.10
Protein Clusters United States 160unstable6.22
Kinomer United Kingdom 49alive5.44
PMDB - Protein Model Database Italy 194unstable1.94
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65unstable3.41
GTOP - Genomes TO Protein Structures and Functions database Japan 26unstable2.72
PiSite - Database of Protein Interaction Sites Japan 28alive3.11
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive8.33
Voronoia - Voronoia Germany 52alive5.78
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive3.78
PMAP - The Proteolysis MAP United States 31unstable1.89
PhyloPat - Phylogenetic Patterns Netherlands 26alive2.17
Pseudofam - pseudogene families database United States 20alive2.20
DNAReplication - DNAReplication United Kingdom 10alive1.09
GISSD - Group I Intron Sequence and Structure Database China 54unstable3.29
UgMicroSatdb - Database for mining microsatellites from Unigenes India 13unstable1.18
ProSAS - Protein Structure and Alternative Splicing database Germany 24unstable0.74
PPT-DB - protein property prediction and testing database Canada 15alive1.50
PairsDB - Pairs Database United Kingdom 17dead0.00
U12DB - U12DB Spain 83alive7.47
ncRNAdb - Noncoding RNAs database Poland 53alive4.82
PhenomicDB - A multi-species genotype-phenotype database for comparative phenomics Germany 121unstable3.72
PROTCOM - Protein Complexes United States 53dead0.00
PlasmID - Plasmid Information Database United States 27alive2.41
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.50
TransportDB - TransportDB United States 298alive27.09
TMBETA-GENOME Japan 20dead0.00
NMPDR - National Microbial Pathogen Data Resource United States 90unstable7.45
OrthoMCL-DB - Querying a Comprehensive Multi-species Collection of Ortholog Groups United States 516unstable30.10
PUMA2 - PUMA2 United States 72dead0.00
Pathguide - the Pathway Resource List United States 310alive25.57
pSTIING United Kingdom 47alive3.92
PepSeeker - A database of proteome peptide identifications for investigating fragmentation patterns United Kingdom 38dead0.00
EPGD - Eukaryotic Paralog Group Database China 16unstable0.27
INSDC - International Nucleotide Sequence Database Collaboration United Kingdom 157alive22.43
dbSNP - Single Nucleotide Polymorphism Database United States 3381unstable62.28
PDBFlex United States 1unstable0.47
EBI - The European Bioinformatics Institute United Kingdom 610unstable16.52
probeBase - probeBase Austria 804unstable49.85
NCBI - National Center for Biotechnology Information United States 16174unstable305.51
JuncDB Israel 1alive0.50
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive4.50
PDBe - Protein Data Bank in Europe United Kingdom 239alive29.88
ENA - European Nucleotide Archive United Kingdom 2398unstable73.08
GSA - Genome Sequence Archive China 4alive3.84
RAID - RNA Association Interaction Database China 34alive8.50
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive1.33
LinkProt Poland 0unstable0.00
PDBj - Protein Data Bank Japan Japan 94unstable0.70
ECOD - Evolutionary Classification of Protein Domains United States 33alive8.25
FAIRDOMHub United Kingdom 0unstable0.00
HieranoiDB Sweden 0alive0.00
GWAS Catalog United Kingdom 3886unstable405.87
Proteome-pI - Proteome Isoelectric Point Database Germany 1alive1.00
HPIDB - Host - Pathogen Interaction Database United States 79alive9.78
PhyloPro Canada 9alive1.26
CCProf Taiwan 0alive0.00
3CDB - Chromosome Conformation Capture Database China 1unstable0.40
UbiNet - Ubiquitylation Networks Taiwan 1alive0.49
DDRprot Spain 2unstable0.38
SeriPort India 0alive0.00
Carotenoids Database - Carotenoids Database Japan 0alive0.00
cMapper Korea Rep. 0alive0.00
* Citations derived from Google Scholar.
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