Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
AnimalTFDB - Animal Transcription Factors Database China 82alive15.91
TFClass - Classification of Human Transcription Factors and Mouse Orthologs Germany 48unstable11.40
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive45.38
UniProt - The Universal Protein Resource United Kingdom 13605alive1036.07
InterPro - Protein sequence analysis & classification United Kingdom 5033alive296.06
CDD - Conserved Domain Database
United States 4407unstable286.45
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive60.39
InParanoid - ortholog groups with inparalogs Sweden 1253alive103.37
OMA - The Orthologous Matrix project United Kingdom 153alive24.74
SMART - Simple Modular Architecture Research Tool
Germany 3106alive161.84
COG - Clusters of Orthologous Genes United States 11125unstable289.25
MoonProt - Moonlighting Proteins Database United States 20alive10.00
TOPDB - Topology Database of Transmembrane Proteins
Hungary 57unstable5.45
TopFIND - Termini oriented protein Function Inferred Database Canada 98alive16.33
REBASE - The Restriction Enzyme Database United States 927alive66.21
NrichD - Remote Homology Detection using Enriched Databases
India 7alive2.33
KnotProt - A database of proteins with knots and slipknots
Poland 67alive13.40
MobiDB - A Database of Protein Disorder and Mobility Annotations Italy 80alive15.84
MatrixDB - The extracellular matrix interaction database France 4alive1.98
MiCroKiTS - Midbody,Centrosome,Kinetochore,Telomere and Spindle China 29alive4.14
RaftProt - Mammalian Lipid Raft Proteome Database Australia 0alive0.00
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable3.76
SASBDB - Small Angle Scattering Biological Data Bank Germany 0alive0.00
ValidatorDB - Database of validation
Czech Republic 0alive0.00
CATH
United Kingdom 1488alive104.16
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable5.64
Platinum - Protein-ligand affinity change upon mutation United Kingdom 0unstable0.00
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive4.80
sc-PDB - An Annotated Database of Druggable Binding Sites from the Protein DataBank
France 165alive14.70
IMGT - Knowledge resource specialized in the immunoglobulins or antibodies France 22alive4.36
IPD - Immuno Polymorphism Database United Kingdom 323alive26.38
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive116.49
STRING - Known and Predicted Protein-Protein Interactions
Switzerland 9248alive544.00
EzCatDB - Database of Enzyme Catalytic Mechanisms
Japan 60unstable3.85
Binding MOAD - Binding Mother of All Databases
United States 148alive12.21
BioGRID - Biological General Repository for Interaction Datasets
Canada 4359alive396.27
Complex Portal
United Kingdom 0alive0.00
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
PTMcode Germany 56alive14.00
dbSNO - Database for Cysteine S-Nitrosylation Taiwan 52alive10.09
ProteomeScout United States 0unstable0.00
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
P2CS - Prokaryotic 2-Component Systems France 80alive9.90
HIV-1 Human Interaction Database United States 171unstable9.88
Viral Genomes - Viral Genomes United States 0unstable0.00
VirHostNet - Virus-Host Network France 93unstable9.88
VirusMentha - VirusMentha Italy 0alive0.00
MyMpn - The Mycoplasma pneumoniae database Spain 11unstable4.95
TrypanoCyc - Trypanosoma brucei Database France 0alive0.00
Ensembl - Ensembl United Kingdom 12662alive827.25
UCSC Genome Browser - University of California, Santa Cruz Genome Browser United States 6429alive459.21
Genomicus - Genomes in Evolution France 182alive25.74
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable11.08
RGD - Rat Genome Database United States 60alive29.70
neXtProt - Exploring the universe of human proteins Switzerland 237unstable17.06
The UCSC Cancer Genomics Browser United States 187unstable6.78
CancerPPD
India 0alive0.00
Cancer3D United States 10alive4.95
MethHC - A database of DNA Methylation and gene expression in Human Cancer Taiwan 18alive8.91
T3DB - The Toxin and Toxin Target Database Canada 73alive10.43
Super Natural II
Germany 11alive5.50
AHTPDB - Database of Antihypertensive Peptides India 7alive3.50
PLAZA - An online platform for plant comparative genomics Belgium 196unstable23.27
Araport - Arabidopsis Information Portal United States 9unstable1.30
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
GOA database - Gene Ontology Annotation (UniProt-GOA) Database
United Kingdom 229alive44.88
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161alive20.13
Cyclebase - Cell-cycle Database Denmark 105alive11.20
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.00
JASPAR Canada 2924alive220.42
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking Portugal 793alive71.37
OnTheFly - TF and TFBS On The Fly United States 9unstable1.17
BloodChIP Australia 11unstable1.65
Network portal - A Database for Storage, Analysis and Visualization of Biological Networks
United States 14alive4.67
Pfam - Protein Families Database United Kingdom 19906alive995.30
eggNOG - Database of Orthologous Groups and Functional Annotation
Germany 107alive35.31
Gene3D - Gene3D United Kingdom 194alive21.56
LenVarDB - Database of length variant protein domains
India 2alive0.67
TCDB - Transporter Classification Database United States 87alive29.00
ELM - The Eukaryotic Linear Motif Resource Germany 325unstable14.30
FireDB - Database of Annotated Functionally Important Residues
Spain 59alive5.90
HRaP - Occurrence of HomoRepeats and Patterns in Eukaryotic and Bacterial Proteomes Russian Federation 6alive1.96
SIMAP - The Similarity Matrix of Proteins
Canada 7unstable1.96
SCOPe - Structural Classification of Proteins-extended
United States 83alive27.39
SCOP2 - Structural Classification of Proteins 2
United Kingdom 50alive16.67
ArchDB
Spain 84alive6.46
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature
Japan 43alive8.60
pE-DB - Protein Ensemble Database Belgium 55unstable16.87
ModBase - Database of Comparative Protein Structure Models
United States 990alive65.34
MP:PD - Packing Database of Membrane Proteins
Germany 5alive1.65
RepeatsDB - A Database of Tandem Repeat Protein Annotations
Italy 33alive10.89
iPfam - Catalog of Protein Family Interactions
United States 38unstable9.25
3did - 3-Dimensional Interacting Domains
Spain 399alive31.92
FunCoup - Database of Genome-wide Functional Coupling Networks.
Sweden 73alive14.31
KBDOCK
France 7alive2.31
Negatome - The Negatome Database
Germany 109unstable14.79
STITCH - Search Tool for Interacting Chemicals
Germany 624alive69.33
UniHI - Unified Human Interactome Portugal 194alive19.40
GPCRDB - G Protein-coupled Receptor (GPCR) Database Denmark 964alive50.23
CentrosomeDB Spain 58alive7.11
SelenoDB
Germany 43alive4.78
Hemolytik - Database of Hemolytic peptides India 13alive4.33
CSA - Catalytic Site Atlas
United Kingdom 614alive45.34
CAZy - Carbohydrate-active Enzymes Database
France 553alive184.33
EKPD - Database of Eukaryotic Protein Kinases China 12alive4.00
MEROPS - The peptidase Database United Kingdom 1760unstable111.02
ASD - Allosteric Database
China 94alive15.67
MultitaskProtDB - Multitasking Proteins DataBase
Spain 18alive6.00
SFLD - Structure Function Linkage Database
United States 231alive20.79
HoPaCI-DB - The Host-Pseudomonas and Coxiella Interaction database France 3unstable0.94
SporeWeb Netherlands 11alive3.67
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive19.68
MycoCosm - The fungal genomics resource United States 93alive29.76
AspGD - Aspergillus Gene Database United States 117alive23.17
SGD - Saccharomyces Genome Database United States 772alive154.40
LoQAtE - The localization and quantitation atlas of the yeast proteome Israel 8alive2.61
mVOC - Microbial volatile organic compound database Germany 38alive12.67
RefSeq - Reference Sequence Database United States 6794unstable207.82
VEGA - Vertebrate Genome Annotation United Kingdom 368alive30.36
WormBase - WormBase Canada 2150alive134.38
CellFinder Germany 5alive1.67
PPD - Plasma Proteome Database India 53unstable16.25
canSAR United Kingdom 70unstable13.30
ChEMBL
United Kingdom 1746unstable324.76
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22alive7.33
AVPdb
India 16alive5.33
CAMP - Collection of Anti-Microbial Peptides
India 218alive30.52
Gramene - A comparative resource for plants United States 79alive26.33
P3DB - Plant Protein Phosphorylation DataBase United States 129alive16.13
ENCODE - Encyclopedia of DNA Elements United States 2053unstable45.80
APPRIS - Annotating Principal Splice Isoforms Spain 39alive9.75
SwissRegulon - A Database of Genome-wide Annotations of Regulatory Sites Switzerland 118unstable8.61
NCBI Epigenomics - NCBI Epigenomics United States 51unstable2.55
Voronoia4RNA - Voronoia for RNA
Germany 4unstable0.51
dbPTM - Database of Protein Post-Translational Modifications
Taiwan 205alive18.64
MetalPDB - Meta knowledge on Protein Data Bank
Italy 18alive4.50
eProS - Energy Profile Suite
Germany 4unstable0.40
SwissSidechain - A Molecular and Structural Database of Non-natural Sidechains
Switzerland 16alive4.00
TOPPR - The Online Protein Processing Resource Belgium 9unstable1.98
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions Taiwan 21unstable4.83
PROSITE - Database of protein domains, families and functional sites Switzerland 8754alive336.69
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive213.50
TIGRFAMs - TIGR defined protein families
United States 940unstable53.46
CyanoLyase
France 10alive2.45
ClusterMine360 Canada 26alive6.43
DoBISCUIT - Database of BIoSynthesis clusters CUrated and InTegrated
Japan 27alive6.75
EENdb - Database of Engineered EndoNucleases China 35alive8.40
ESTHER - The database of ESTerases and alpha/beta-Hydrolase Enzymes and Relatives
France 47unstable3.17
PeroxiBase France 333alive30.27
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive5.50
ZiFDB - Zinc Finger Database United States 73dead0.00
ChemProt - Chemical-protein Interaction Database
Denmark 97alive15.84
GFDB - Glycan Fragment Database
United States 10alive2.50
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive12.50
D2P2 - Database of Disordered Protein Prediction United Kingdom 80alive19.80
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.55
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive37.85
DGA - Database of Disease and Gene Annotations China 23alive5.75
BioGPS
United States 99alive24.75
PaVE - PapillomaVirus Episteme United States 83unstable8.72
ECMDB - Escherichia coli Metabolome Database Canada 32alive8.00
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive5.94
dictyBase - Database for Dictyostelium Discoideum United States 128alive16.00
CFGP - Comparative Fungal Genomics Platform Korea Rep. 102unstable7.59
MonarchBase - The Monarch Butterfly Genome Database United States 23unstable5.41
enzyme portal - enzyme portal
United Kingdom 13alive3.25
WholeCellKB - WholeCellKB United States 16alive4.00
HMDB - The Human Metabolome Database Canada 2615alive261.50
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive45.40
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable23.48
SynSysNet - Synaptic Proteins Database Germany 18alive4.50
TissueNet - The Database of Human Tissue Protein-Protein Interactions Israel 53alive12.99
ZFIN - Zebrafish Information Network United States 899alive44.50
PRIDE - PRoteomics IDEntifications United Kingdom 846alive205.15
LUCApedia - Last Universal Common Ancestor United States 10unstable2.38
IUPHAR-DB United Kingdom 144alive23.52
BioLiP
United States 63alive15.75
G4LDB - G-quadruplex ligands database China 24unstable2.94
NPACT - Naturally occuring Plant based Anticancerous Compound-Activity-Target DataBase India 70alive5.38
SwissBioisostere - A Database of Molecular Replacements for Ligand Design
Switzerland 30alive7.43
TropGeneDB - tropical gene database France 34alive2.54
PhosPhAt - The Arabidopsis Protein Phosphorylation Site Database Germany 416alive46.22
SUBA - The SUBcellular localisation Database for Arabidopsis Proteins Australia 168alive42.00
OrysPSSP - A Comparative Platform for Small Secreted Proteins from Rice and Other Plants China 8unstable1.48
InnateDB Canada 339unstable30.89
ScerTF - Saccharomyces cerevisia Transcription Factors Database United States 35unstable4.06
CharProtDB - Characterized Protein Database
United States 21unstable3.70
MnM - Minimotif Miner
United States 231unstable14.28
MimoDB - Mimotope Database
China 76unstable9.99
SitEx Russian Federation 5alive0.99
ProtoNet Israel 187alive13.09
BYKdb - Bacteria Tyrosine Kinase Database
France 15unstable0.93
ConoServer - Database for Conopeptides Australia 205unstable18.68
DD - Database of Death Domain Korea Rep. 14alive2.80
MIPModDB - Major Intrinsic Protein Database
India 23alive4.60
OPM - Orientations of Proteins in Membranes Database
United States 142alive28.40
NucleaRDB - Information System for Nuclear Receptors
Netherlands 209unstable3.66
ProGlycProt - Prokaryotic Glycoproteins India 13alive2.52
ProRepeat Netherlands 10unstable0.50
SCRIPDB
Canada 7alive1.39
MMDB - Macromolecular Database
United States 79unstable8.22
AH-DB - Apo and Holo Structures DataBase
Taiwan 9alive1.80
CAPS-DB
United Kingdom 7alive1.40
ccPDB - Compilation and Creation of datasets from PDB
India 12alive2.40
Cube-DB - Cube-DB Singapore 3alive0.60
the DARC site - The Database for Aligned Ribosomal Complexes site Germany 4unstable0.71
DOMMINO - Database of MacroMolecular Interactions
United States 14unstable0.81
IndelFR - Indel Flanking Region Database
China 12dead0.00
NRG-CING - NMR Restraints Grid -Common Interface for NMR structure Generation
Netherlands 29unstable1.28
STAP
Korea Rep. 11alive2.18
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
HFV - Hemorrhagic Fever Viruses (HFV) Database United States 9alive1.78
ViPR - virus pathogene resourse United States 57alive11.40
VFDB - Virulence Factor Database China 448alive37.33
FungiDB - FungiDB United States 47alive9.40
Nematode - Nematode.net United States 163alive12.54
FunTree - FunTree
United Kingdom 23alive4.46
MACiE - Mechanism, Annotation and Classification in Enzymes
United Kingdom 45alive8.64
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive3.40
HotRegion Turkey 23alive4.60
IBIS - Inferred Biomolecular Interactions Server
United States 33alive6.60
InterEvol
France 15alive2.97
MINT - Molecular Interaction Database
Italy 312unstable56.78
PINA - Protein Interaction Network Analysis Australia 281unstable23.53
Newt-omics - A Comprehensive Repository for Omics Data from the Newt notophthalmus viridescens Germany 20alive4.00
HGPD - Human Gene and Protein Database Japan 36alive4.50
dbDEPC - Database of Differentially Expressed Proteins in Human Cancer China 22unstable2.95
NCG - Network of Cancer Genes Italy 51alive10.20
UMD-BRCA1/BRCA2 - Universal mutation database-BRCA1/BRCA2 France 23dead0.00
DAMPD - Dragon Antimicrobial Peptide Database South Africa 39unstable4.91
MitoMiner - A database of the mitochondrial proteome
United Kingdom 97alive12.00
DIGIT - Database of ImmunoGlobulins with Integrated Tools Italy 19alive3.69
DNAtraffic - DNAtraffic Poland 3unstable0.52
ExoCarta - EXOSOME PROTEIN, RNA AND LIPID DATABASE
Australia 590alive73.75
Gene Wiki - Gene Wiki United States 113unstable4.68
EcoliWiki - EcoliWiki United States 24unstable4.42
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.69
AREsite - AU-rich Elements Site Austria 110alive18.15
ASPicDB - Alternative Splicing Database
Italy 75dead0.00
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36unstable5.70
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive5.39
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable5.12
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable3.03
PSORTdb Canada 191unstable13.37
PHOSIDA - phosphorylation site database Germany 567unstable53.30
Phospho.ELM - A database of experimentally verified phosphorylation sites in eukaryotic proteins Germany 580unstable9.82
Phospho3D Spain 62alive6.01
PolyQ - Polyglutamine Australia 18unstable2.49
PRIDB - Protein-RNA Interface Database United States 49unstable7.27
IsoBase - IsoRank PPI Network Alignment Based Ortholog Database United States 44alive7.33
RBPDB - The Database of RNA-binding Protein Specificities Canada 133alive22.17
OMPdb - A database of ß-barrel outer membrane proteins from Gram-negative bacteria Greece 28alive4.62
PREX - PeroxiRedoxin classification indEX United States 47alive7.83
ThYme - Thioester-active Enzymes
United States 30alive5.00
TMPad - The TransMembrane Protein Helix-Packing Database
Taiwan 18unstable1.92
VKCDB - voltage-gated potassium channels databse Canada 34alive2.62
BriX
Belgium 78alive11.14
BSDB - Bio-molecule Stretching Database
Poland 21alive3.47
CDDB - Conformational Dynamics Databank
United States 11unstable0.95
PCDB - A database of protein conformational diversity Argentina 18alive2.97
PCDDB - Protein Circular Dichroism Data Bank United Kingdom 91alive8.27
SAHG - Structure Atlas of Human Genome Japan 8unstable0.95
TOPSAN - The Open Protein Structure Annotation Network
United States 63unstable6.12
PRO - Protein Ontology United States 163alive26.62
Effective - Effective Germany 48alive7.92
ArachnoServer - ArachnoServer Australia 131dead0.00
BISC - BInary SubComplex Database
United Kingdom 3unstable0.20
DIMA - Domain Interaction MAp
Germany 69unstable4.52
DOMINE - Database of Protein Domain Interaction
United States 205unstable19.13
DroID - Drosophila Interactions Database United States 183alive20.33
HitPredict Japan 57alive9.50
KUPS - University of Kansas Proteomics Service United States 21unstable0.59
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.67
ProtCID - Protein Common Interfaces Database United States 44alive7.26
RegPhos - Regulatory Network in Protein Phosphorylation Taiwan 49alive8.09
REPAIRtoire - A Database of DNA Repair Pathways Poland 24alive3.96
CIPRO - Ciona Intestinalis Protein Database Japan 25alive4.17
The Autophagy Database Japan 25dead0.00
CPLM - Compendium of Protein Lysine Modifications
China 27unstable1.22
FragmentStore - FragmentStore
Germany 11alive1.83
HIT - Herbal Ingredients' Targets Database China 60unstable7.40
PROMISCUOUS Germany 109alive18.17
Protegen - Protective Antigens United States 28unstable4.06
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701alive50.07
AtPID - Arabidopsis thaliana Protein Interactome Database China 136alive14.51
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.17
iRefWeb - Literature curation of protein interactions
Canada 66alive7.19
GATMD - GABA Transporter Mutagenesis Database United States 7dead0.00
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.98
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.86
PDBWiki Germany 24alive3.43
BrainTrap - Fly Brain Protein Trap Database United Kingdom 14alive1.96
OpenFluDB - A Database for Human and Animal Influenza Virus Switzerland 17alive2.43
PhosphoGRID Canada 63unstable4.32
GeneCards - GeneCards Israel 900unstable29.37
hUbiquitome - ubiquitination cascades in humans China 14dead0.00
CELLPEDIA Japan 10alive1.67
LccED - The Laccase Engineering Database
Germany 42dead0.00
FunSecKB - Fungal Secretome KnowledgeBase United States 56alive9.24
LPS-annotate Canada 8dead0.03
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.33
Histone Database - Histone Database United States 19unstable0.89
eFIP - eFIPonline
United States 13alive2.55
DFVF - Database of Known Fungal Virulence Factors United States 5alive0.99
MuteinDB - The Mutein Database
Austria 4dead0.00
PRINTS - A compendium of protein fingerprints United Kingdom 42alive8.15
TGD Wiki - Tetrahymena genome database Wiki United States 8alive1.60
Aptamer base - Aptamer database
Canada 21unstable1.22
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.31
wwpdb - worldwide protein data bank archive
United States 8alive1.98
HypoxiaDB - Hypoxia regulated proteins database India 3alive0.74
yApoptosis - yeast apoptosis database Sweden 1alive0.25
The Banana Genome Hub France 19alive4.75
PMP - Protein Model Portal Switzerland 43alive10.75
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.58
SUS-BAR - Statistically Validated Annotation of Sus Scrofa Protein Sequences Italy 2unstable0.41
MisPred - Miss Predict Protein Database Hungary 5unstable1.05
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.62
eFG - Electronic Resource for Fusarium Graminearum China 1alive0.25
FSRD - Fungal Stress Response Database Hungary 8alive1.98
dbPPT - Database of Protein Phosphorylation in Plants China 5alive1.67
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
CBMAR - Comprehensive Beta-lactamase Molecular Annotation Resource
India 2unstable0.25
AromaDeg - Aromatic Hydrocarbon Degradation Database
Germany 8alive2.67
HProtDB - Halophile Protein Database India 1unstable0.25
BactPepDB - Bacteria Peptide Database France 3alive0.98
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable1.24
RLIMS-P - A Rule-based Literature Mining System for Protein Phosphorylation
United States 8alive2.67
PTM-SD - Post Translational Modification Structural Database France 6alive2.00
dbCRY - Cryptochrome Database
Korea Rep. 2unstable0.49
FixPred - FixPred
Hungary 1unstable0.28
BambooGDB - Bamboo Genome Database China 12unstable2.84
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.58
Kin-Driver Argentina 7unstable2.19
WholeCellSimDB United States 4unstable1.19
PlantCAZyme - A database for plant carbohydrate-active enzymes United States 3unstable0.95
aglgenes - aglgenes Israel 0alive0.00
PLIC - Protein-Ligand Interaction Clusters India 3alive0.99
HPVdb - Human Papillomavirus T cell Antigen Database United States 11alive3.67
BCL2DB - BCL-2 Database
France 4unstable0.39
COMPARTMENTS - Subcellular localization database
Germany 29alive9.28
ProtoBug - An automatic hierarchical classification of insect proteomes Israel 1alive0.50
NeuroPep - A Comprehensive Resource of Neuropeptides
China 3alive1.50
CyanOmics - Cyanobacterial Omics Analysis Database China 0alive0.00
EpiDBase - EpiDBase
India 1unstable0.35
LMPID - Linear Motif mediated Protein Protein Interaction Database India 1alive0.50
CHOPIN United Kingdom 1alive0.50
dbPSP - Database for Protein Phosphorylation Sites in Prokaryotes China 0alive0.00
Follicle Online - Follicle Online
China 1dead0.00
novPTMenzy - A Database for Enzymes Involved in Novel Post-translational Modifications.
India 1unstable0.45
3DGD - 3D Genome Database China 6unstable1.00
IEDB - The Immune Epitope Database United States 28alive4.62
NeuroPedia - Neuropeptide Database United States 15alive2.42
PathLocdb - Pathway Localization Database China 10unstable0.39
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
PhosphoNetworks United States 11alive3.67
3D-interologs - 3D-domain interactions based on homologous proteins
Taiwan 18alive2.57
SeqDepot
United States 1alive0.33
Sinbase - Sesamum indicum database China 14unstable6.09
HIPdb - Database of HIV inhibiting peptides India 19alive4.75
Plant-PrAS - Plant-Protein Annotation Suite Japan 4alive2.00
PolysacDB India 4alive0.80
SKPDB - ShiKimate Pathway DataBase Brazil 22dead0.00
IIIDB - database for isoform-isoform interactions and isoform network modules
United States 0alive0.00
LEAPdb - Late Embryogenesis Abundant Proteins
France 30alive4.16
LipidHome - database of theoretical lipids optimized for high throughput mass spectrometry lipidomics
United Kingdom 20unstable4.75
SyStemCell China 6unstable1.04
YRC PIR - The Yeast Resource Center Public Image Repository United States 20alive2.86
WALTZ-DB - database of amyloid-forming peptides Belgium 0alive0.00
MCG - Maize Cell Genomics Database United States 4alive2.00
TassDB2 - TAndem Splice Site DataBase Germany 45alive4.45
MTTD - Medicago Truncatula Transporter database China 6unstable0.80
MUFOLD-DB - A Solution For Protein 3D Structure Prediction
United States 1alive0.33
mpMoRFsDB - Database of Molecular Recognition Features in Membrane Proteins
Greece 6alive1.49
wDBTF - Inventory Database of Wheat Transcription Factor France 19unstable1.93
MPIC - Mitochondrial Protein Import Components Database Australia 5alive2.50
RedoxDB - protein oxidative modification database Hong Kong SAR China 25alive5.00
mUbiSiDa - Database of mammalian protein ubiquitination site China 14unstable4.43
TRIP - TRansient receptor potential channel-Interacting Protein
Korea Rep. 34alive5.55
TumorHoPe - Tumor Homing Peptide Database
India 29alive5.80
CoDNaS - Conformational Diversity of Native State
Argentina 19unstable1.71
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.85
UniVIO - Uniformed Viewer for Integrative Omics Japan 13alive3.25
PrionHome Canada 9dead0.04
ProFITS - Protein Families Involved in the Transduction of Signalling China 7alive0.97
PupDB - database of pupylated proteins Taiwan 23alive4.55
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive8.25
dbTEU - DataBase of Trace Element Utilization United States 14alive1.98
GPCR-RD - A Database For Experimental Restaints Of GPCRs United States 38alive5.43
DetoxiProt - An integrated database of detoxification proteins China 3unstable0.47
HSC-explorer - hematopoietic stem cell explorer Germany 6unstable1.31
CLIPdb China 0alive0.00
CyanoPhyChe India 2alive0.40
DBBP - DataBase of Binding Pairs in protein-nucleic acid interactions Skip Navigation Links
Korea Rep. -unstable-
ExTopoDB - Experimentally derived topological models of transmembrane proteins
Greece 10alive1.41
footprintDB - footprintDB
Spain 9alive3.00
IRView - Database and viewer of interacting regions (IRs) in protein sequences Japan 1alive0.20
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.25
NMPdb - Database of Nuclear Matrix Proteins.
United States 53dead0.00
SPD - Secreted Protein Database China 119unstable5.75
eBLOCKs - eBLOCKs
United States 28dead0.00
PDBSITE Russian Federation 92alive7.59
ADDA
Finland 44dead0.00
FunShift
Sweden 44alive3.67
PRECISE - Predicted and Consensus Interaction Sites in Enzymes United States 16dead0.00
ProDom France 251alive20.92
S4
United Kingdom 20dead0.00
SBASE
Italy 23unstable1.30
SYSTERS
Germany 51unstable2.38
PDB-Ligand Korea Rep. 58unstable1.98
CSS - Carbohydrate Structure Suite
Germany 121dead0.00
GenDiS - Genomic Distribution of Protein Structural Domain Superfamilies India 16alive1.33
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343alive27.44
STING Report
Brazil 22alive1.83
PFD - Protein Folding Database Australia 30unstable1.55
Integr8
United Kingdom 169alive13.80
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive32.69
CYGD - Comprehensive Yeast Genome Database Germany 327unstable21.53
PROPHECY - PROfiling of PHEnotypic Characteristics in Yeast Sweden 29alive2.42
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive4.25
3D-footprint
Spain 34alive4.86
RegPrecise - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes United States 141unstable18.73
TransmiR - TF–miRNA Regulatory Database
China 184alive26.29
MeMotif - A wiki for motifs in transmembrane proteins
Germany 15alive2.14
SuperCYP
Germany 102alive14.57
FunSimMat - Functional Similarity Matrix
Germany 87alive9.57
ComSin
Russian Federation 22alive3.08
fPOP - footprinting Pockets Of Proteins
United States 11dead0.00
PGD - Protein Geometry Database United States 19unstable2.31
PTGL - Protein Topology Graph Library Germany 10dead0.00
PNU - Protein Naming Utility United States 6unstable0.78
DynaProt 2D - Proteome Database of Lactococcus lactis Germany 15alive1.25
MetaRouter - Bioinformatics for Bioremediation United Kingdom 38alive3.13
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive3.17
AMPDB - Arabidopsis Mitochondrial Protein Database Australia 68alive5.67
MiST2 - Microbial Signal Transduction Database United States 147unstable19.53
FlyTF - Transcription factor datamine for Drosophila melanogaster United Kingdom 128unstable9.89
MetaBioME - Comprehensive Metagenomic BioMining Engine Japan 36alive5.14
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database United States 94dead0.00
CORUM - Comprehensive Resource of Mammalian protein complexes Germany 269alive37.28
DP - Dynamic Proteomics Israel 15dead0.00
GWIDD - Genome-wide Protein Docking Database
United States 30alive4.20
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60alive8.57
HRTBLDb - Hormone Receptors Target Binding Loci Database United States 9dead0.00
Peptidome United States 30dead0.00
PSI-MR - Protein Structure Initiative Material Repository United States 105alive15.00
AtNoPDB - Arabidopsis Nucleolar Protein Database United Kingdom 61unstable4.83
GeneFarm - GeneFarm France 22dead0.00
PeroxisomeDB - PEROXISOME database Spain 61alive8.63
PlnTFDB - Plant Transcription Factor Database Germany 246alive34.79
SALAD Japan 36alive4.99
AntigenDB
India 35unstable4.75
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable180.71
CyBase
Australia 220unstable8.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable10.26
REFOLD
Australia 81dead0.00
LOCATE - subcellular localization database Australia 87alive7.91
NOPdb - Nucleolar Proteome Database United Kingdom 96dead0.00
NURSA - Nuclear Receptor Signaling Atlas
United States 93alive8.45
PAZAR - A public database of transcription factor and regulatory sequence annotation Canada 65alive8.13
SitesBase
United Kingdom 91dead0.00
BIOZON
United States 53unstable4.24
MulPSSM - A Database of Multiple Position-specific Scoring Matrices of Protein Domain Families
India 28unstable0.64
SDR - Specificity-determining Residue Database
United States 16dead0.00
SuperSite
Germany 28alive3.43
TMFunction
Japan 23dead0.00
Protein Clusters United States 160unstable10.40
Degradome - The Degradome database Spain 107dead0.00
Kinomer United Kingdom 49alive6.13
EROP - Endogenous Regulatory OligoPeptide knowledgebase
Russian Federation 41alive3.73
DMAPS - Database of Multiple Alignments for Protein Structures
United States 10dead0.00
FSN - Flexible Structural Neighborhood
United States 13alive1.18
iMOTdb - interacting Motif Database
India 3alive0.27
MolMovDB - Database of Macromolecular Movements
United States 652unstable29.85
PMDB - Protein Model Database Italy 194unstable3.17
OKCAM - Ontology for Cell Adhesion Molecules United States 10unstable1.16
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable204.16
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65alive5.67
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.94
CC+
United Kingdom 78alive9.75
ConSurf-DB
Israel 104alive13.00
Circular Permutation Database
Taiwan 36alive4.45
GTOP - Genomes TO Protein Structures and Functions database Japan 26alive3.15
JAIL - Just another interface library
Germany 7alive0.88
KineticDB
Russian Federation 53unstable5.43
PiSite - Database of Protein Interaction Sites Japan 28alive3.50
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive9.38
RsiteDB - RNA binding site database
Israel 19alive2.38
SPROUTS - Structural Prediction for pRotein fOlding UTility System
United States 21dead0.00
Voronoia - Voronoia Germany 52alive6.50
VIPERdb - Virus Particle Explorer United States 293alive26.64
ARDB - Antibiotic Resistance Genes Database
United States 284alive35.15
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive4.25
Genolevures - Genomic Exploration of the Hemiascomycete Yeasts France 223unstable5.15
ExplorEnz - The Enzyme Database
Ireland 54alive6.75
Bionemo - Biodegradation Network Molecular Biology Database
Spain 15alive1.88
PMAP - The Proteolysis MAP United States 31unstable3.02
PIPs - human protein–protein interaction prediction database United Kingdom 114alive14.25
ExDom - ExDom United States 10unstable0.39
Pseudofam - pseudogene families database United States 20alive2.47
HPRD - Human Protein Reference Database India 3067unstable201.55
Human Proteinpedia India 65unstable7.47
CTdatabase - Cancer-Testis Database Brazil 116alive14.07
MoKCa - Mutations, Oncogenes, Knowledge & Cancer United Kingdom 34alive4.21
AutDB - Autism Spectrum Disorders database United States 121unstable13.76
DNAReplication - DNAReplication United Kingdom 10alive1.21
Sys-BodyFluid China 57unstable1.85
APD - Antimicrobial Peptide Database United States 572alive70.07
GabiPD - GABI Primary Database Germany 36alive4.32
PhytAMP - antimicrobial plant peptides Tunisia 105unstable2.10
ProSAS - Protein Structure and Alternative Splicing database Germany 24unstable1.25
DBTBS - Database of Transcriptional Regulation in Bacillus subtilis Japan 495alive30.94
TAIR - The Arabidopsis Information Resource United States 768unstable67.41
PlantTribes United States 57alive6.14
Mitome - A Database for Comparative Mitochondrial Genomics in Metazoan Animals
Korea Rep. 34alive3.78
LigASite
Belgium 57dead0.00
Bacteriome.org - Bacteriome.org Canada 46unstable3.27
BMRB - Biological Magnetic Resonance Data Bank
United States 635alive70.56
BioHealthBase United States 70unstable7.31
GenoList - An Integrated Environment for the Analysis of Microbial Genomes France 50unstable4.44
ToxoDB - Toxoplasma gondii database United States 381alive27.21
MALISAM - Manual Alignments For Structurally Analogous Motifs
United States 20alive2.20
MegaMotifbase - Structural Motifs in Protein Families and Superfamilies
India 24alive2.67
PPT-DB - protein property prediction and testing database Canada 15alive1.67
PairsDB - Pairs Database United Kingdom 17dead0.00
ChromDB - The chromatin database United States 72unstable4.56
DB-PABP - DB-PABP
United States 4dead0.00
NORINE - A Database of Nonribosomal Peptides
France 171unstable16.53
Telomerase Database - Telomerase Database
United States 94alive10.34
GDB:Structures - Glycoconjugate Data Bank:Structures
Japan 33alive3.67
Greglist - Database of G-quadruplex Regulated Genes China 43unstable3.87
QuadBase - QuadBase India 71unstable7.34
SGDB - Synthetic Gene Database
United States 26unstable1.27
PharmGED - Pharmacogenetic Effect Database Singapore 8dead0.00
MAPU - Max-Planck Unified proteome database Germany 53alive5.30
SynDB - Synapse protein DataBase
China 35unstable2.03
PROTCOM - Protein Complexes United States 53dead0.00
SNAPPI-DB - SNAPPI-DB
United Kingdom 60alive6.00
GeneSpeed - GeneSpeed database United States 10dead0.00
WormBook - the online review of Caenorhabditis elegans biology United States 51alive5.10
DOMINO - DOMINO
Italy 72unstable1.66
LMSD - LIPID MAPS Structure Database
United States 279alive27.90
CYCLONET - CYCLONET
Russian Federation 15alive1.50
CutDB
United States 84alive8.15
BindingDB - BindingDB
United States 706alive69.19
eSLDB - eSLDB Italy 45alive4.50
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.82
GeneTrees - A Phylogenomics Resource For Prokaryotes United States 11dead0.00
SISYPHUS - SISYPHUS
United Kingdom 72alive7.20
Defensins knowledgebase - Defensins knowledgebase
Singapore 81alive8.10
Sentra - Sentra United States 20dead0.00
TransportDB - TransportDB United States 298alive29.80
GlycoMapsDB - GlycoMapsDB Germany 46alive4.60
TMBETA-GENOME Japan 20dead0.00
T-DB - TOPOFIT-DB
United States 19dead0.00
euHCVdb - European HCV Database United States 118unstable3.42
INVHOGEN - INVertebrate HOmologous GENes Germany 5dead0.00
LEGER - Post-genome Database for Listeria Research Germany 24unstable1.59
MPact - MIPS Protein Interaction Resource on Yeast Germany 357unstable15.58
SGCEdb United States 2dead0.00
LMPD - LIPID MAPS Proteome Database
United States 43alive3.91
AffinDB - Affinity database for protein-ligand complexes
Germany 84alive7.64
pSTIING United Kingdom 47alive4.27
MfunGD - MIPS Mouse Functional Genome Database Germany 14unstable0.64
PepSeeker - A database of proteome peptide identifications for investigating fragmentation patterns United Kingdom 38dead0.00
PeptideAtlas United States 839alive75.51
ChloroplastDB - Chloroplast Genome Database United States 68alive6.06
MitoP2 - An integrative tool for the analysis of the mitochondrial proteome Germany 156dead0.00
Epitome - Epitome
United States 58unstable3.69
NetworKIN - A Resource for Exploring Cellular Phosphorylation Networks Canada 195alive21.67
DisProt - Database of Protein Disorder United States 838alive69.14
COMBREX-DB - COMBREX database United States 0alive0.00
RBP-Var China 0alive0.00
PDBFlex United States 1alive1.00
SIB - Swiss Institute of Bioinformatics
Switzerland 6alive1.94
BIGNASim - BIGNASim database structure and analysis portal for nucleic acids simulation data
Spain 1alive1.00
UET - Universal Evolutionary Trace United States 1alive0.98
MutationAligner - A Resource of Recurrent Mutation Hotspots in Protein Domains in Cancer United States 0unstable0.00
SBR-Blood - Systems Biology Repository United States 0unstable0.00
EffectiveDB - EffectiveDB Austria 0alive0.00
MitoAge - A database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity Israel 1alive1.00
EBI - The European Bioinformatics Institute United Kingdom 610alive25.99
CPPsite - Database of Cell-Penetrating Peptides
India 70alive14.00
iGNM - Gaussian Network Model Database United States 116alive9.67
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.96
EMDataBank - Unified Data Resource for 3-Dimensional Electron Microscopy
United States 1alive0.99
SugarBindDB - SugarBind Database Switzerland 10alive2.50
DBAASP - Database of Antimicrobial Activity and Structure of Peptides Georgia 9alive3.00
Start2Fold Belgium 1alive1.00
GEneSTATION United States 1alive0.98
NCBI - National Center for Biotechnology Information United States 16174unstable485.22
ONRLDB - Orphan Nuclear Receptor Ligand Binding Database
India 0alive0.00
ProPepper Hungary 0dead0.00
MicRhoDE - Microbial Rhodopsin database for Diversity and Evolution studies France 1alive0.48
MetazSecKB - Metazoa (Human/Animal) Secretome and Subcellular Proteome KnowledgeBase United States 0alive0.00
EpiFactors - EpiFactors Russian Federation 3alive1.49
EvoDB - Evolutionary rates DataBase
South Africa 0unstable0.00
SInCRe - Structural Interactome Computational Resource United Kingdom 0alive0.00
BEAN - Bacterial Effector Analyzer China 0alive0.00
FARE-CAFE - Database of Functional and Regulatory Elements of Cancer-Associated Fusion Events Taiwan 1unstable0.38
SATPdb - A database of structurally annotated therapeutic peptides
India 1alive1.00
RBCC - Red Blood Cell Collection Hungary 1alive0.50
dbHiMo - database for histone-modifying enzymes
Korea Rep. 0alive0.00
Ebola-KB - Ebola virus-centered Knowledge Base United States 0alive0.00
mycoCLAP - Characterized Lignocellulose-Active Proteins of Fungal Origin Canada 0unstable0.00
KIR - Kiwifruit Information Resource China 0alive0.00
JuncDB Israel 1alive0.98
READDB - RNA Binding Protein Expression and Disease Dynamics database
United States 0alive0.00
HCSD - Human Cancer Secretome Database Sweden 1unstable0.47
IID - Integrated interactions database Canada 1alive0.99
NBDB - Nucleotide binding database
Singapore 1alive0.99
BDB - Biopanning Data Bank
China 0unstable0.00
Colorectal Cancer Atlas Australia 1alive1.00
KLIFS Netherlands 2alive1.96
PDBe - Protein Data Bank in Europe United Kingdom 239alive34.14
iPPI-DB - Inhibitors of Protein–Protein Interaction Database
France 9alive9.00
SIDER - Side Effect Resource
Germany 2alive2.00
PlantPAN - Plant Promoter Analysis Navigator Taiwan 188alive20.89
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.96
GtoPdb - IUPHAR/BPS Guide to PHARMACOLOGY United Kingdom 2alive1.94
MitoCarta - An Inventory of Mammalian Mitochondrial Genes United States 2unstable1.52
HCVpro - Hepatitis C Virus Protein Interaction Database South Africa -unstable-
POSTAR - POST-trAnscriptional Regulation China 1alive0.97
ADPriboDB - The Database of ADP-ribosylated proteins United States 0alive0.00
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive2.00
LinkProt Poland 0alive0.00
Membranome - Membrane Proteome United States 1unstable0.59
mutLBSgeneDB - mutated Ligand Binding Site gene DataBase
United States 1alive1.00
WERAM - Writers, Erasers and Readers of Acetylation & Methylation China 1alive1.00
PDBj - Protein Data Bank Japan Japan 94unstable2.01
ECOD - Evolutionary Classification of Protein Domains United States 33alive11.00
TSTMP - Target Selection for human TransMembrane Proteins
Hungary 0alive0.00
IRD - Influenza Research Database United States 165dead0.00
dbSAP - Single Amino Acid Polymorphism Database China 0alive0.00
PlaMoM - Plant Mobile Macromolecules Hong Kong SAR China 1unstable0.90
PX - ProteomeXchange
United Kingdom 1059unstable307.11
jPOSTrepo
Japan 0dead0.00
Proteome-pI - Proteome Isoelectric Point Database Germany 1alive1.00
SinEx DB - SinEx DATABASE Chile 0alive0.00
PvTFDB - Phaseolus vulgaris Transcription Factor Database India 0alive0.00
PhyloPro Canada 9unstable1.43
HistoneDB - histone database
United States 4dead0.00
KinetochoreDB
Australia 0dead0.00
CCProf Taiwan 0alive0.00
UbiNet - Ubiquitylation Networks Taiwan 1unstable0.95
CoopTFD - Cooperative Transcription Factors Database Taiwan 1unstable0.93
Tfcheckpoint - Transcription Factor Checkpoint Norway 8alive2.00
3DFlu Poland 0alive0.00
MAHMI - Mechanism of Action of the Human MIcrobiome Spain 0unstable0.00
FARME DB - Functional Antibiotic Resistance Metagenomic Element Database
United States 0alive0.00
VerSeDa - Vertebrate Secretome Database Spain 0alive0.00
TMPL - Transmembrane protein Models Positioned in the Lipid bilayer
France 0alive0.00
BISQUE - Biological Sequence Exchange United States 1alive1.00
TOPDOM - database of conservatively located domains and motifs in proteins
Hungary 27alive3.00
* Citations derived from Google Scholar.
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