Database Commons a catalog of biological databases

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Data type:

Database name Data type(s) Major organism(s) Location Citation* Status z-index
NCBI Gene - NCBI Gene United States 1802unstable72.08
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive4.75
ProteomeScout United States 0unstable0.00
P2CS - Prokaryotic 2-Component Systems France 80alive9.90
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive30.60
Ensembl - Ensembl United Kingdom 12662alive827.25
Pfam - Protein Families Database United Kingdom 19906alive995.30
pE-DB - Protein Ensemble Database Belgium 55unstable16.87
LPSN - List of Prokaryotic names with standing in nomenclature United States 129alive43.00
POGO-DB - Database of Pairwise-comparisons Of Genomes and universal Orthologous genes United States 4alive1.33
DOOR - Database of Prokaryotic Operons United States 218alive26.98
PhylomeDB - Phylome DataBase Spain 241alive26.78
GeneTack database - GeneTack database United States 6dead0.00
PROSITE - Database of protein domains, families and functional sites Switzerland 8754alive336.69
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive213.50
The Genome Properties database - The Genome Properties database United States 65unstable14.95
PeroxiBase France 333alive30.27
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive37.85
GenColors - GenColors Germany 17alive1.40
PRIDE - PRoteomics IDEntifications United Kingdom 846unstable190.35
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
ProOpDB - Prokaryotic Operon DataBase Mexico 61alive11.96
PRIDB - Protein-RNA Interface Database United States 49unstable7.35
PREX - PeroxiRedoxin classification indEX United States 47alive7.83
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
PSSRdb - Polymorphic Simple Sequence Repeats database India 6unstable0.59
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
PROMISCUOUS Germany 109alive18.17
HOMD - The Human Oral Microbiome Database United States 216alive30.86
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.86
PDBWiki Germany 24alive3.43
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
PolyprOnline France 2unstable0.63
PTM-SD - Post Translational Modification Structural Database France 6alive2.00
PhylOPDb - phylogenetic oligonucleotide probe database France 24unstable4.18
PLIC - Protein-Ligand Interaction Clusters India 3alive0.99
dbPSP - Database for Protein Phosphorylation Sites in Prokaryotes China 0alive0.00
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
PupDB - database of pupylated proteins Taiwan 23alive4.55
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
RegPrecise - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes United States 141unstable18.73
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
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
PRODORIC - PROcariotIC Database Of Gene-Regulation Germany 52unstable5.59
PseudoBase++ - An extension of PseudoBase United States 38alive4.75
Protein Clusters United States 160unstable9.80
PMDB - Protein Model Database Italy 194unstable2.82
PiSite - Database of Protein Interaction Sites Japan 28alive3.50
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive9.38
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive4.25
PMAP - The Proteolysis MAP United States 31unstable2.87
PhyloPat - Phylogenetic Patterns Netherlands 26alive2.36
ProTISA China 25dead0.00
HEG-DB - The highly expressed genes database Spain 271alive26.02
PPT-DB - protein property prediction and testing database Canada 15alive1.67
PairsDB - Pairs Database United Kingdom 17dead0.00
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
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 310alive27.90
pSTIING United Kingdom 47alive4.27
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 104unstable2.91
PDBFlex United States 1alive1.00
probeBase - probeBase Austria 804unstable51.69
NCBI - National Center for Biotechnology Information United States 16174unstable447.16
Pre_GI - Predicted Genomic Islands database South Africa 0alive0.00
5SRNAdb - Database of of ribosomal 5S RNAs Poland 9alive9.00
SigMol India 1alive0.98
PDBe - Protein Data Bank in Europe United Kingdom 239alive34.14
ENA - European Nucleotide Archive United Kingdom 2398unstable107.91
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 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
CCProf Taiwan 0alive0.00
3CDB - Chromosome Conformation Capture Database China 1unstable0.55
DDRprot Spain 2unstable0.54
SeriPort India 0alive0.00
cMapper Korea Rep. 0alive0.00
* Citations derived from Google Scholar.