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 1802unstable60.99
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive3.96
ProteomeScout United States 0unstable0.00
P2CS - Prokaryotic 2-Component Systems France 80alive8.80
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive28.05
Ensembl - Ensembl United Kingdom 12662alive775.55
Pfam - Protein Families Database United Kingdom 19906alive947.90
pE-DB - Protein Ensemble Database Belgium 55unstable12.79
LPSN - List of Prokaryotic names with standing in nomenclature United States 129alive32.25
POGO-DB - Database of Pairwise-comparisons Of Genomes and universal Orthologous genes United States 4alive1.00
DOOR - Database of Prokaryotic Operons United States 218alive23.98
PhylomeDB - Phylome DataBase Spain 241alive24.10
GeneTack database - GeneTack database United States 6dead0.00
PROSITE - Database of protein domains, families and functional sites Switzerland 8754alive317.74
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive170.80
The Genome Properties database - The Genome Properties database United States 65unstable11.96
PeroxiBase France 333alive27.75
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive35.14
GenColors - GenColors Germany 17alive1.29
PRIDE - PRoteomics IDEntifications United Kingdom 846unstable138.74
GeneDB - GeneDB United Kingdom 92alive15.18
ProtoNet Israel 187alive12.22
Polbase - Polymerase Database United States 8unstable0.33
ProRepeat Netherlands 10unstable0.35
PASS2 - Protein Alignments organised as Structural Superfamilies India 70alive4.38
Pocketome United States 54alive8.91
ProtChemSI - protein-chemical structural interactions Germany 9alive1.49
PSCDB - Protein Structural Change DataBase Japan 35alive5.00
ProOpDB - Prokaryotic Operon DataBase Mexico 61alive9.86
PRIDB - Protein-RNA Interface Database United States 49unstable6.37
PREX - PeroxiRedoxin classification indEX United States 47alive6.71
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 163alive22.82
PhEVER - phylogenetic exploration of virues' evolutionary relationships France 4unstable0.07
PSSRdb - Polymorphic Simple Sequence Repeats database India 6unstable0.46
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
PROMISCUOUS Germany 109alive15.57
HOMD - The Human Oral Microbiome Database United States 216alive27.00
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.63
PDBWiki Germany 24alive3.00
Histone Database - Histone Database United States 19unstable0.65
PRINTS - A compendium of protein fingerprints United Kingdom 42unstable6.65
PMP - Protein Model Portal Switzerland 43unstable7.48
PolyprOnline France 2unstable0.47
PTM-SD - Post Translational Modification Structural Database France 6alive1.50
PhylOPDb - phylogenetic oligonucleotide probe database France 24unstable3.52
PLIC - Protein-Ligand Interaction Clusters India 3alive0.74
dbPSP - Database for Protein Phosphorylation Sites in Prokaryotes China 0alive0.00
PathLocdb - Pathway Localization Database China 10unstable0.29
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
RedoxDB - protein oxidative modification database Hong Kong SAR China 25alive4.13
PupDB - database of pupylated proteins Taiwan 23alive3.80
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. 58unstable1.56
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343unstable22.16
PFD - Protein Folding Database Australia 30unstable1.22
RegPrecise - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes United States 141unstable16.22
PGD - Protein Geometry Database United States 19unstable1.73
PTGL - Protein Topology Graph Library Germany 10dead0.00
PNU - Protein Naming Utility United States 6unstable0.69
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60alive7.50
Peptidome United States 30dead0.00
PSI-MR - Protein Structure Initiative Material Repository United States 105alive13.13
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.14
ProTherm - Thermodynamic Database for Proteins and Mutants Japan 618dead0.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable10.65
PAZAR - A public database of transcription factor and regulatory sequence annotation Canada 65alive7.22
PRODORIC - PROcariotIC Database Of Gene-Regulation Germany 52unstable5.03
PseudoBase++ - An extension of PseudoBase United States 38alive4.05
Protein Clusters United States 160unstable8.00
PMDB - Protein Model Database Italy 194unstable2.42
PiSite - Database of Protein Interaction Sites Japan 28alive3.11
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive8.33
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive3.78
PMAP - The Proteolysis MAP United States 31unstable2.34
PhyloPat - Phylogenetic Patterns Netherlands 26alive2.17
ProTISA China 25dead0.00
HEG-DB - The highly expressed genes database Spain 271alive23.65
PPT-DB - protein property prediction and testing database Canada 15alive1.50
PairsDB - Pairs Database United Kingdom 17dead0.00
PhenomicDB - A multi-species genotype-phenotype database for comparative phenomics Germany 121unstable4.75
PROTCOM - Protein Complexes United States 53dead0.00
PlasmID - Plasmid Information Database United States 27alive2.38
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.64
GeneTrees - A Phylogenomics Resource For Prokaryotes United States 11dead0.00
Sentra - Sentra United States 20dead0.00
ICDS database - Interrupted CoDing Sequence database France 23dead0.00
PUMA2 - PUMA2 United States 72dead0.00
SIDDBASE United States 14dead0.00
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
RegTransBase - a database of regulatory sequences and interactions United States 104unstable2.46
PDBFlex United States 1alive0.50
probeBase - probeBase Austria 804unstable48.78
NCBI - National Center for Biotechnology Information United States 16174unstable395.36
Pre_GI - Predicted Genomic Islands database South Africa 0alive0.00
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive4.50
SigMol India 1alive0.49
PDBe - Protein Data Bank in Europe United Kingdom 239alive29.88
ENA - European Nucleotide Archive United Kingdom 2398unstable94.78
KGCAK - A K-mer based database for genome-wide phylogeny and complexity evaluation China 0unstable0.00
MethSMRT China 0unstable0.00
RAID - RNA Association Interaction Database China 34alive8.50
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive1.33
LinkProt Poland 0alive0.00
PDBj - Protein Data Bank Japan Japan 94unstable1.18
ECOD - Evolutionary Classification of Protein Domains United States 33alive8.25
FAIRDOMHub United Kingdom 0unstable0.00
HieranoiDB Sweden 0alive0.00
GWAS Catalog United Kingdom 3886alive431.78
Proteome-pI - Proteome Isoelectric Point Database Germany 1alive1.00
HPIDB - Host - Pathogen Interaction Database United States 79alive9.78
CCProf Taiwan 0alive0.00
3CDB - Chromosome Conformation Capture Database China 1unstable0.32
DDRprot Spain 2unstable0.32
SeriPort India 0alive0.00
cMapper Korea Rep. 0alive0.00
* Citations derived from Google Scholar.
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