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 1802unstable72.08
UniProt - The Universal Protein Resource United Kingdom 13605alive1036.07
InterPro - Protein sequence analysis & classification United Kingdom 5033alive296.06
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive60.39
OMA - The Orthologous Matrix project United Kingdom 153unstable22.95
COG - Clusters of Orthologous Genes United States 11125unstable272.56
MBGD - Microbial Genome Database Japan 279alive19.73
MobiDB - A Database of Protein Disorder and Mobility Annotations Italy 80alive15.84
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable3.72
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive4.75
PTMcode Germany 56alive14.00
ProteomeScout United States 0unstable0.00
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable51.69
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive30.60
Ensembl - Ensembl United Kingdom 12662alive827.25
DDMGD - database of diseases associated gene methylation in different species Saudi Arabia 2unstable0.87
diArk - Database for Eukaryotic Genome Research Germany 16alive1.60
uORFdb - upstream open reading frames database Germany 22unstable5.79
Pfam - Protein Families Database United Kingdom 19906alive995.30
ELM - The Eukaryotic Linear Motif Resource Germany 325unstable13.00
pE-DB - Protein Ensemble Database Belgium 55unstable16.87
EKPD - Database of Eukaryotic Protein Kinases China 12alive4.00
DEG - Database of Essential Genes China 573alive44.08
SILVA - High quality ribosomal RNA databases Germany 3927unstable129.59
RefSeq - Reference Sequence Database United States 6794unstable195.83
PhylomeDB - Phylome DataBase Spain 241alive26.78
Dfam - Dfam United States 58unstable9.86
UCNEbase - A database of ultraconserved non-coding elements and genomic regulatiory blocks Switzerland 20alive5.00
GeneTack database - GeneTack database United States 6dead0.00
PROSITE - Database of protein domains, families and functional sites Switzerland 8754alive336.69
KEGG OC - KEGG Ortholog Cluster Japan 37alive9.25
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive213.50
PeroxiBase France 333alive30.27
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive5.50
ZiFDB - Zinc Finger Database United States 73dead0.00
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive37.85
PR2 - Protist Ribosomal Reference Database France 80alive20.00
metaMicrobesOnline - Phylogenomic Analysis of Microbial Communities United States 5alive1.24
GEO - Gene Expression Omnibus United States 9384unstable306.54
PRIDE - PRoteomics IDEntifications United Kingdom 846unstable190.35
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.98
GeneDB - GeneDB United Kingdom 92alive18.22
ProtoNet Israel 187alive13.09
Polbase - Polymerase Database United States 8unstable0.43
ProRepeat Netherlands 10unstable0.46
PASS2 - Protein Alignments organised as Structural Superfamilies India 70alive4.67
Pocketome United States 54alive10.69
ProtChemSI - protein-chemical structural interactions Germany 9alive1.78
PSCDB - Protein Structural Change DataBase Japan 35alive5.83
GOLD - Genomes On Line Database United States 1646unstable40.40
UniPathway - UniPathway Switzerland 54unstable7.13
WikiPathways - WikiPathways Netherlands 228unstable28.73
RNAMDB - RNA Modification Database United States 1297unstable34.40
Phospho.ELM - A database of experimentally verified phosphorylation sites in eukaryotic proteins Germany 580unstable9.37
Phospho3D Spain 62alive6.01
PRIDB - Protein-RNA Interface Database United States 49unstable7.35
PREX - PeroxiRedoxin classification indEX United States 47alive7.83
VKCDB - voltage-gated potassium channels databse Canada 34alive2.62
PCDB - A database of protein conformational diversity Argentina 18alive2.97
PCDDB - Protein Circular Dichroism Data Bank United Kingdom 91alive8.27
PRO - Protein Ontology United States 163alive26.62
PhEVER - phylogenetic exploration of virues' evolutionary relationships France 4unstable0.10
Pathway Commons - Search and visualize public biological pathway information United States 395alive65.83
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.67
ProtCID - Protein Common Interfaces Database United States 44alive7.26
The Autophagy Database Japan 25dead0.00
PROMISCUOUS Germany 109alive18.17
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.86
PDBWiki Germany 24alive3.43
GOOD - Gene-Oriented Ortholog Database Taiwan 3unstable0.35
Histone Database - Histone Database United States 19unstable0.82
PRINTS - A compendium of protein fingerprints United Kingdom 42alive8.06
PMP - Protein Model Portal Switzerland 43unstable10.21
piRBase - piRNA database China 6unstable1.86
PolyprOnline France 2unstable0.63
PTM-SD - Post Translational Modification Structural Database France 6alive2.00
PLIC - Protein-Ligand Interaction Clusters India 3alive0.99
PathLocdb - Pathway Localization Database China 10unstable0.36
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
RedoxDB - protein oxidative modification database Hong Kong SAR China 25alive4.95
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.85
UniCarb-DB - UniCarb-DB Australia 65dead0.00
DeOri - Database of Eukaryotic DNA Replication Origins China 12unstable2.11
TGI - TIGR Gene Index database United States 214alive17.83
UTRdb - UTRdb Italy 644unstable34.47
PDBSITE Russian Federation 92alive7.59
PRECISE - Predicted and Consensus Interaction Sites in Enzymes United States 16dead0.00
ProDom France 251alive20.92
PDB-Ligand Korea Rep. 58unstable1.84
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343unstable25.44
PFD - Protein Folding Database Australia 30unstable1.45
PartiGeneDB - A Database of Partial Genomes Canada 12alive0.99
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive32.69
Recode-2 Ireland 35alive4.95
Polymorphix France 23unstable0.29
IRESite - Internal Ribosome Entry Site Czech Republic 126alive11.11
ITS2 Database - Internal Transcribed Spacer 2 Database Germany 366alive33.27
PGD - Protein Geometry Database United States 19unstable2.14
PTGL - Protein Topology Graph Library Germany 10dead0.00
PNU - Protein Naming Utility United States 6unstable0.79
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60alive8.57
Peptidome United States 30dead0.00
PSI-MR - Protein Structure Initiative Material Repository United States 105alive15.00
PeroxisomeDB - PEROXISOME database Spain 61alive8.63
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable195.17
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.73
ProTherm - Thermodynamic Database for Proteins and Mutants Japan 618dead0.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable10.79
PAZAR - A public database of transcription factor and regulatory sequence annotation Canada 65alive8.13
GtRNAdb - Genomic tRNA Database United States 378alive47.25
PseudoBase++ - An extension of PseudoBase United States 38alive4.75
Protein Clusters United States 160unstable9.80
Kinomer United Kingdom 49alive6.13
PMDB - Protein Model Database Italy 194unstable2.82
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65unstable5.26
GTOP - Genomes TO Protein Structures and Functions database Japan 26alive3.15
PiSite - Database of Protein Interaction Sites Japan 28alive3.50
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive9.38
Voronoia - Voronoia Germany 52alive6.50
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive4.25
PMAP - The Proteolysis MAP United States 31unstable2.87
PhyloPat - Phylogenetic Patterns Netherlands 26alive2.36
Pseudofam - pseudogene families database United States 20alive2.47
DNAReplication - DNAReplication United Kingdom 10alive1.21
GISSD - Group I Intron Sequence and Structure Database China 54unstable4.20
UgMicroSatdb - Database for mining microsatellites from Unigenes India 13alive1.44
ProSAS - Protein Structure and Alternative Splicing database Germany 24unstable1.17
PPT-DB - protein property prediction and testing database Canada 15alive1.67
PairsDB - Pairs Database United Kingdom 17dead0.00
U12DB - U12DB Spain 83alive8.22
ncRNAdb - Noncoding RNAs database Poland 53alive5.30
PhenomicDB - A multi-species genotype-phenotype database for comparative phenomics Germany 121unstable5.65
PROTCOM - Protein Complexes United States 53dead0.00
PlasmID - Plasmid Information Database United States 27alive2.62
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.76
TransportDB - TransportDB United States 298alive29.80
TMBETA-GENOME Japan 20dead0.00
NMPDR - National Microbial Pathogen Data Resource United States 90unstable8.55
OrthoMCL-DB - Querying a Comprehensive Multi-species Collection of Ortholog Groups United States 516unstable28.61
PUMA2 - PUMA2 United States 72dead0.00
Pathguide - the Pathway Resource List United States 310alive27.90
pSTIING United Kingdom 47alive4.27
PepSeeker - A database of proteome peptide identifications for investigating fragmentation patterns United Kingdom 38dead0.00
EPGD - Eukaryotic Paralog Group Database China 16unstable0.43
INSDC - International Nucleotide Sequence Database Collaboration United Kingdom 157alive26.17
dbSNP - Single Nucleotide Polymorphism Database United States 3381unstable92.04
PDBFlex United States 1alive1.00
EBI - The European Bioinformatics Institute United Kingdom 610unstable23.87
probeBase - probeBase Austria 804unstable51.69
NCBI - National Center for Biotechnology Information United States 16174unstable447.16
JuncDB Israel 1alive0.99
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive9.00
PDBe - Protein Data Bank in Europe United Kingdom 239alive34.14
ENA - European Nucleotide Archive United Kingdom 2398unstable107.91
GSA - Genome Sequence Archive China 4alive4.00
RAID - RNA Association Interaction Database China 34alive11.33
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive2.00
LinkProt Poland 0alive0.00
PDBj - Protein Data Bank Japan Japan 94unstable1.61
ECOD - Evolutionary Classification of Protein Domains United States 33alive11.00
FAIRDOMHub United Kingdom 0unstable0.00
HieranoiDB Sweden 0alive0.00
GWAS Catalog United Kingdom 3886alive485.75
Proteome-pI - Proteome Isoelectric Point Database Germany 1alive1.00
HPIDB - Host - Pathogen Interaction Database United States 79alive11.17
PhyloPro Canada 9alive1.44
CCProf Taiwan 0alive0.00
3CDB - Chromosome Conformation Capture Database China 1unstable0.55
UbiNet - Ubiquitylation Networks Taiwan 1alive0.96
DDRprot Spain 2unstable0.54
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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