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 82alive13.12
TFClass - Classification of Human Transcription Factors and Mouse Orthologs Germany 48unstable7.78
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive40.33
UniProt - The Universal Protein Resource United Kingdom 13605alive962.07
InterPro - Protein sequence analysis & classification United Kingdom 5033alive279.61
CDD - Conserved Domain Database
United States 4407unstable220.35
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive56.84
InParanoid - ortholog groups with inparalogs Sweden 1253alive95.42
OMA - The Orthologous Matrix project United Kingdom 153unstable18.14
SMART - Simple Modular Architecture Research Tool
Germany 3106alive153.75
COG - Clusters of Orthologous Genes United States 11125unstable238.39
MoonProt - Moonlighting Proteins Database United States 20alive6.53
TOPDB - Topology Database of Transmembrane Proteins
Hungary 57unstable4.22
TopFIND - Termini oriented protein Function Inferred Database Canada 98alive14.00
REBASE - The Restriction Enzyme Database United States 927alive61.80
NrichD - Remote Homology Detection using Enriched Databases
India 7alive1.75
KnotProt - A database of proteins with knots and slipknots
Poland 67alive11.17
MobiDB - A Database of Protein Disorder and Mobility Annotations Italy 80alive13.20
MatrixDB - The extracellular matrix interaction database France 4alive1.32
MiCroKiTS - Midbody,Centrosome,Kinetochore,Telomere and Spindle China 29alive3.63
RaftProt - Mammalian Lipid Raft Proteome Database Australia 0alive0.00
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable2.48
SASBDB - Small Angle Scattering Biological Data Bank Germany 0alive0.00
ValidatorDB - Database of validation
Czech Republic 0alive0.00
CATH
United Kingdom 1488alive97.22
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable4.99
Platinum - Protein-ligand affinity change upon mutation United Kingdom 0unstable0.00
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive3.96
sc-PDB - An Annotated Database of Druggable Binding Sites from the Protein DataBank
France 165alive13.34
IMGT - Knowledge resource specialized in the immunoglobulins or antibodies France 22alive3.63
IPD - Immuno Polymorphism Database United Kingdom 323unstable20.62
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive99.85
STRING - Known and Predicted Protein-Protein Interactions
Switzerland 9248alive513.78
EzCatDB - Database of Enzyme Catalytic Mechanisms
Japan 60unstable3.69
Binding MOAD - Binding Mother of All Databases
United States 148alive11.27
BioGRID - Biological General Repository for Interaction Datasets
Canada 4359unstable316.03
Complex Portal
United Kingdom 0unstable0.00
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
PTMcode Germany 56alive11.20
dbSNO - Database for Cysteine S-Nitrosylation Taiwan 52alive8.41
ProteomeScout United States 0unstable0.00
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
P2CS - Prokaryotic 2-Component Systems France 80alive8.80
HIV-1 Human Interaction Database United States 171unstable7.52
Viral Genomes - Viral Genomes United States 0unstable0.00
VirHostNet - Virus-Host Network France 93unstable8.99
VirusMentha - VirusMentha Italy 0alive0.00
MyMpn - The Mycoplasma pneumoniae database Spain 11unstable3.34
TrypanoCyc - Trypanosoma brucei Database France 0alive0.00
Ensembl - Ensembl United Kingdom 12662alive775.55
UCSC Genome Browser - University of California, Santa Cruz Genome Browser United States 6429alive428.60
Genomicus - Genomes in Evolution France 182alive22.52
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable8.68
RGD - Rat Genome Database United States 60alive19.40
neXtProt - Exploring the universe of human proteins Switzerland 237unstable12.24
The UCSC Cancer Genomics Browser United States 187unstable5.19
CancerPPD
India 0alive0.00
Cancer3D United States 10alive3.30
MethHC - A database of DNA Methylation and gene expression in Human Cancer Taiwan 18alive5.94
T3DB - The Toxin and Toxin Target Database Canada 73alive9.13
Super Natural II
Germany 11alive3.67
AHTPDB - Database of Antihypertensive Peptides India 7alive2.33
PLAZA - An online platform for plant comparative genomics Belgium 196unstable17.64
Araport - Arabidopsis Information Portal United States 9unstable0.75
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
GOA database - Gene Ontology Annotation (UniProt-GOA) Database
United Kingdom 229unstable31.68
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161alive17.53
Cyclebase - Cell-cycle Database Denmark 105unstable8.61
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.00
JASPAR Canada 2924alive204.68
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking Portugal 793alive65.42
OnTheFly - TF and TFBS On The Fly United States 9unstable0.74
BloodChIP Australia 11unstable1.04
Network portal - A Database for Storage, Analysis and Visualization of Biological Networks
United States 14alive3.50
Pfam - Protein Families Database United Kingdom 19906alive947.90
eggNOG - Database of Orthologous Groups and Functional Annotation
Germany 107alive26.48
Gene3D - Gene3D United Kingdom 194alive19.40
LenVarDB - Database of length variant protein domains
India 2alive0.50
TCDB - Transporter Classification Database United States 87alive21.53
ELM - The Eukaryotic Linear Motif Resource Germany 325unstable9.75
FireDB - Database of Annotated Functionally Important Residues
Spain 59alive5.36
HRaP - Occurrence of HomoRepeats and Patterns in Eukaryotic and Bacterial Proteomes Russian Federation 6alive1.46
SIMAP - The Similarity Matrix of Proteins
Canada 7unstable1.26
SCOPe - Structural Classification of Proteins-extended
United States 83alive20.54
SCOP2 - Structural Classification of Proteins 2
United Kingdom 50alive12.38
ArchDB
Spain 84alive6.00
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature
Japan 43alive7.17
pE-DB - Protein Ensemble Database Belgium 55unstable12.79
ModBase - Database of Comparative Protein Structure Models
United States 990alive61.26
MP:PD - Packing Database of Membrane Proteins
Germany 5alive1.24
RepeatsDB - A Database of Tandem Repeat Protein Annotations
Italy 33alive8.17
iPfam - Catalog of Protein Family Interactions
United States 38unstable5.89
3did - 3-Dimensional Interacting Domains
Spain 399unstable25.17
FunCoup - Database of Genome-wide Functional Coupling Networks.
Sweden 73alive11.92
KBDOCK
France 7alive1.70
Negatome - The Negatome Database
Germany 109unstable12.94
STITCH - Search Tool for Interacting Chemicals
Germany 624alive62.40
UniHI - Unified Human Interactome Portugal 194alive17.64
GPCRDB - G Protein-coupled Receptor (GPCR) Database Denmark 964alive47.72
CentrosomeDB Spain 58alive6.19
SelenoDB
Germany 43alive4.30
Hemolytik - Database of Hemolytic peptides India 13alive3.25
CSA - Catalytic Site Atlas
United Kingdom 614unstable37.28
CAZy - Carbohydrate-active Enzymes Database
France 553alive138.25
EKPD - Database of Eukaryotic Protein Kinases China 12alive3.00
MEROPS - The peptidase Database United Kingdom 1760unstable88.00
ASD - Allosteric Database
China 94alive13.43
MultitaskProtDB - Multitasking Proteins DataBase
Spain 18alive4.50
SFLD - Structure Function Linkage Database
United States 231alive19.06
HoPaCI-DB - The Host-Pseudomonas and Coxiella Interaction database France 3unstable0.71
SporeWeb Netherlands 11alive2.75
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive17.49
MycoCosm - The fungal genomics resource United States 93unstable19.07
AspGD - Aspergillus Gene Database United States 117alive19.31
SGD - Saccharomyces Genome Database United States 772alive128.67
LoQAtE - The localization and quantitation atlas of the yeast proteome Israel 8alive1.96
mVOC - Microbial volatile organic compound database Germany 38alive9.50
RefSeq - Reference Sequence Database United States 6794unstable169.85
VEGA - Vertebrate Genome Annotation United Kingdom 368alive28.02
WormBase - WormBase Canada 2150alive126.47
CellFinder Germany 5alive1.25
PPD - Plasma Proteome Database India 53unstable12.32
canSAR United Kingdom 70alive11.20
ChEMBL
United Kingdom 1746unstable229.89
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22alive5.50
AVPdb
India 16alive4.00
CAMP - Collection of Anti-Microbial Peptides
India 218alive26.70
Gramene - A comparative resource for plants United States 79alive19.75
P3DB - Plant Protein Phosphorylation DataBase United States 129alive13.90
ENCODE - Encyclopedia of DNA Elements United States 2053unstable36.66
APPRIS - Annotating Principal Splice Isoforms Spain 39alive7.80
SwissRegulon - A Database of Genome-wide Annotations of Regulatory Sites Switzerland 118unstable6.65
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.89
Voronoia4RNA - Voronoia for RNA
Germany 4unstable0.46
dbPTM - Database of Protein Post-Translational Modifications
Taiwan 205alive16.91
MetalPDB - Meta knowledge on Protein Data Bank
Italy 18alive3.60
eProS - Energy Profile Suite
Germany 4unstable0.27
SwissSidechain - A Molecular and Structural Database of Non-natural Sidechains
Switzerland 16alive3.20
TOPPR - The Online Protein Processing Resource Belgium 9unstable1.57
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions Taiwan 21unstable3.86
PROSITE - Database of protein domains, families and functional sites Switzerland 8754alive317.74
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive170.80
TIGRFAMs - TIGR defined protein families
United States 940unstable50.87
CyanoLyase
France 10alive1.96
ClusterMine360 Canada 26alive5.15
DoBISCUIT - Database of BIoSynthesis clusters CUrated and InTegrated
Japan 27alive5.40
EENdb - Database of Engineered EndoNucleases China 35unstable6.65
ESTHER - The database of ESTerases and alpha/beta-Hydrolase Enzymes and Relatives
France 47unstable3.20
PeroxiBase France 333alive27.75
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive4.40
ZiFDB - Zinc Finger Database United States 73dead0.00
ChemProt - Chemical-protein Interaction Database
Denmark 97alive13.30
GFDB - Glycan Fragment Database
United States 10alive2.00
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive10.00
D2P2 - Database of Disordered Protein Prediction United Kingdom 80alive15.84
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.14
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive35.14
DGA - Database of Disease and Gene Annotations China 23alive4.60
BioGPS
United States 99alive19.80
PaVE - PapillomaVirus Episteme United States 83unstable5.98
ECMDB - Escherichia coli Metabolome Database Canada 32alive6.40
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive4.75
dictyBase - Database for Dictyostelium Discoideum United States 128alive14.22
CFGP - Comparative Fungal Genomics Platform Korea Rep. 102unstable5.92
MonarchBase - The Monarch Butterfly Genome Database United States 23unstable4.37
enzyme portal - enzyme portal
United Kingdom 13unstable2.24
WholeCellKB - WholeCellKB United States 16alive3.20
HMDB - The Human Metabolome Database Canada 2615alive237.73
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive39.72
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable16.56
SynSysNet - Synaptic Proteins Database Germany 18alive3.60
TissueNet - The Database of Human Tissue Protein-Protein Interactions Israel 53alive10.39
ZFIN - Zebrafish Information Network United States 899alive42.38
PRIDE - PRoteomics IDEntifications United Kingdom 846unstable138.74
LUCApedia - Last Universal Common Ancestor United States 10unstable1.62
IUPHAR-DB United Kingdom 144alive20.16
BioLiP
United States 63alive12.60
G4LDB - G-quadruplex ligands database China 24unstable2.69
NPACT - Naturally occuring Plant based Anticancerous Compound-Activity-Target DataBase India 70alive5.00
SwissBioisostere - A Database of Molecular Replacements for Ligand Design
Switzerland 30alive5.94
TropGeneDB - tropical gene database France 34alive2.36
PhosPhAt - The Arabidopsis Protein Phosphorylation Site Database Germany 416alive41.60
SUBA - The SUBcellular localisation Database for Arabidopsis Proteins Australia 168alive33.60
OrysPSSP - A Comparative Platform for Small Secreted Proteins from Rice and Other Plants China 8unstable1.20
InnateDB Canada 339unstable28.81
ScerTF - Saccharomyces cerevisia Transcription Factors Database United States 35unstable2.92
CharProtDB - Characterized Protein Database
United States 21unstable3.15
MnM - Minimotif Miner
United States 231unstable12.90
MimoDB - Mimotope Database
China 76unstable8.84
SitEx Russian Federation 5alive0.81
ProtoNet Israel 187alive12.22
BYKdb - Bacteria Tyrosine Kinase Database
France 15unstable0.95
ConoServer - Database for Conopeptides Australia 205unstable17.42
DD - Database of Death Domain Korea Rep. 14alive2.33
MIPModDB - Major Intrinsic Protein Database
India 23alive3.83
OPM - Orientations of Proteins in Membranes Database
United States 142alive23.67
NucleaRDB - Information System for Nuclear Receptors
Netherlands 209unstable2.95
ProGlycProt - Prokaryotic Glycoproteins India 13alive2.10
ProRepeat Netherlands 10unstable0.35
SCRIPDB
Canada 7alive1.16
MMDB - Macromolecular Database
United States 79unstable5.92
AH-DB - Apo and Holo Structures DataBase
Taiwan 9alive1.50
CAPS-DB
United Kingdom 7alive1.17
ccPDB - Compilation and Creation of datasets from PDB
India 12alive2.00
Cube-DB - Cube-DB Singapore 3alive0.50
the DARC site - The Database for Aligned Ribosomal Complexes site Germany 4unstable0.61
DOMMINO - Database of MacroMolecular Interactions
United States 14unstable0.91
IndelFR - Indel Flanking Region Database
China 12unstable0.12
NRG-CING - NMR Restraints Grid -Common Interface for NMR structure Generation
Netherlands 29unstable0.87
STAP
Korea Rep. 11alive1.82
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
HFV - Hemorrhagic Fever Viruses (HFV) Database United States 9alive1.49
ViPR - virus pathogene resourse United States 57alive9.50
VFDB - Virulence Factor Database China 448alive34.46
FungiDB - FungiDB United States 47alive7.83
Nematode - Nematode.net United States 163alive11.64
FunTree - FunTree
United Kingdom 23alive3.72
MACiE - Mechanism, Annotation and Classification in Enzymes
United Kingdom 45unstable6.38
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive2.83
HotRegion Turkey 23alive3.83
IBIS - Inferred Biomolecular Interactions Server
United States 33alive5.45
InterEvol
France 15alive2.48
MINT - Molecular Interaction Database
Italy 312unstable44.20
PINA - Protein Interaction Network Analysis Australia 281unstable22.48
Newt-omics - A Comprehensive Repository for Omics Data from the Newt notophthalmus viridescens Germany 20alive3.33
HGPD - Human Gene and Protein Database Japan 36alive4.00
dbDEPC - Database of Differentially Expressed Proteins in Human Cancer China 22unstable2.42
NCG - Network of Cancer Genes Italy 51alive8.50
UMD-BRCA1/BRCA2 - Universal mutation database-BRCA1/BRCA2 France 23dead0.00
DAMPD - Dragon Antimicrobial Peptide Database South Africa 39unstable3.58
MitoMiner - A database of the mitochondrial proteome
United Kingdom 97alive10.45
DIGIT - Database of ImmunoGlobulins with Integrated Tools Italy 19alive3.07
DNAtraffic - DNAtraffic Poland 3unstable0.44
ExoCarta - EXOSOME PROTEIN, RNA AND LIPID DATABASE
Australia 590alive65.56
Gene Wiki - Gene Wiki United States 113unstable3.53
EcoliWiki - EcoliWiki United States 24unstable3.40
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
AREsite - AU-rich Elements Site Austria 110alive15.56
ASPicDB - Alternative Splicing Database
Italy 75dead0.00
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36alive4.94
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive4.62
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable4.43
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable2.75
PSORTdb Canada 191unstable12.64
PHOSIDA - phosphorylation site database Germany 567unstable48.45
Phospho.ELM - A database of experimentally verified phosphorylation sites in eukaryotic proteins Germany 580unstable7.87
Phospho3D Spain 62alive5.47
PolyQ - Polyglutamine Australia 18unstable2.19
PRIDB - Protein-RNA Interface Database United States 49unstable6.37
IsoBase - IsoRank PPI Network Alignment Based Ortholog Database United States 44alive6.29
RBPDB - The Database of RNA-binding Protein Specificities Canada 133alive19.00
OMPdb - A database of ß-barrel outer membrane proteins from Gram-negative bacteria Greece 28alive3.96
PREX - PeroxiRedoxin classification indEX United States 47alive6.71
ThYme - Thioester-active Enzymes
United States 30alive4.29
TMPad - The TransMembrane Protein Helix-Packing Database
Taiwan 18unstable1.39
VKCDB - voltage-gated potassium channels databse Canada 34alive2.43
BriX
Belgium 78alive9.56
BSDB - Bio-molecule Stretching Database
Poland 21alive2.97
CDDB - Conformational Dynamics Databank
United States 11unstable0.93
PCDB - A database of protein conformational diversity Argentina 18alive2.55
PCDDB - Protein Circular Dichroism Data Bank United Kingdom 91alive7.58
SAHG - Structure Atlas of Human Genome Japan 8unstable0.70
TOPSAN - The Open Protein Structure Annotation Network
United States 63unstable4.57
PRO - Protein Ontology United States 163alive22.82
Effective - Effective Germany 48alive6.79
ArachnoServer - ArachnoServer Australia 131dead0.00
BISC - BInary SubComplex Database
United Kingdom 3unstable0.15
DIMA - Domain Interaction MAp
Germany 69unstable4.26
DOMINE - Database of Protein Domain Interaction
United States 205unstable14.76
DroID - Drosophila Interactions Database United States 183alive18.30
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.45
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.43
ProtCID - Protein Common Interfaces Database United States 44alive6.22
RegPhos - Regulatory Network in Protein Phosphorylation Taiwan 49alive6.93
REPAIRtoire - A Database of DNA Repair Pathways Poland 24alive3.39
CIPRO - Ciona Intestinalis Protein Database Japan 25alive3.57
The Autophagy Database Japan 25dead0.00
CPLM - Compendium of Protein Lysine Modifications
China 27unstable0.89
FragmentStore - FragmentStore
Germany 11alive1.57
HIT - Herbal Ingredients' Targets Database China 60unstable5.40
PROMISCUOUS Germany 109alive15.57
Protegen - Protective Antigens United States 28unstable3.56
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701alive46.73
AtPID - Arabidopsis thaliana Protein Interactome Database China 136unstable12.65
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.37
iRefWeb - Literature curation of protein interactions
Canada 66alive6.47
GATMD - GABA Transporter Mutagenesis Database United States 7dead0.00
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.73
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.63
PDBWiki Germany 24alive3.00
BrainTrap - Fly Brain Protein Trap Database United Kingdom 14alive1.72
OpenFluDB - A Database for Human and Animal Influenza Virus Switzerland 17alive2.13
PhosphoGRID Canada 63unstable3.23
GeneCards - GeneCards Israel 900unstable23.85
hUbiquitome - ubiquitination cascades in humans China 14dead0.00
CELLPEDIA Japan 10alive1.43
LccED - The Laccase Engineering Database
Germany 42dead0.00
FunSecKB - Fungal Secretome KnowledgeBase United States 56alive7.92
LPS-annotate Canada 8dead0.02
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.00
Histone Database - Histone Database United States 19unstable0.65
eFIP - eFIPonline
United States 13alive2.12
DFVF - Database of Known Fungal Virulence Factors United States 5alive0.82
MuteinDB - The Mutein Database
Austria 4dead0.00
PRINTS - A compendium of protein fingerprints United Kingdom 42unstable6.65
TGD Wiki - Tetrahymena genome database Wiki United States 8alive1.33
Aptamer base - Aptamer database
Canada 21unstable1.12
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.00
wwpdb - worldwide protein data bank archive
United States 8alive1.58
HypoxiaDB - Hypoxia regulated proteins database India 3alive0.59
yApoptosis - yeast apoptosis database Sweden 1alive0.20
The Banana Genome Hub France 19alive3.80
PMP - Protein Model Portal Switzerland 43unstable7.48
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.15
SUS-BAR - Statistically Validated Annotation of Sus Scrofa Protein Sequences Italy 2unstable0.28
MisPred - Miss Predict Protein Database Hungary 5unstable0.86
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.42
eFG - Electronic Resource for Fusarium Graminearum China 1alive0.20
FSRD - Fungal Stress Response Database Hungary 8alive1.58
dbPPT - Database of Protein Phosphorylation in Plants China 5alive1.25
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
CBMAR - Comprehensive Beta-lactamase Molecular Annotation Resource
India 2unstable0.16
AromaDeg - Aromatic Hydrocarbon Degradation Database
Germany 8alive2.00
HProtDB - Halophile Protein Database India 1unstable0.17
BactPepDB - Bacteria Peptide Database France 3alive0.74
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable0.93
RLIMS-P - A Rule-based Literature Mining System for Protein Phosphorylation
United States 8unstable1.80
PTM-SD - Post Translational Modification Structural Database France 6alive1.50
dbCRY - Cryptochrome Database
Korea Rep. 2unstable0.31
FixPred - FixPred
Hungary 1unstable0.22
BambooGDB - Bamboo Genome Database China 12unstable1.80
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.38
Kin-Driver Argentina 7unstable1.63
WholeCellSimDB United States 4unstable0.91
PlantCAZyme - A database for plant carbohydrate-active enzymes United States 3unstable0.69
aglgenes - aglgenes Israel 0alive0.00
PLIC - Protein-Ligand Interaction Clusters India 3alive0.74
HPVdb - Human Papillomavirus T cell Antigen Database United States 11alive2.75
BCL2DB - BCL-2 Database
France 4unstable0.37
COMPARTMENTS - Subcellular localization database
Germany 29unstable5.95
ProtoBug - An automatic hierarchical classification of insect proteomes Israel 1alive0.33
NeuroPep - A Comprehensive Resource of Neuropeptides
China 3alive0.99
CyanOmics - Cyanobacterial Omics Analysis Database China 0alive0.00
EpiDBase - EpiDBase
India 1unstable0.20
LMPID - Linear Motif mediated Protein Protein Interaction Database India 1alive0.33
CHOPIN United Kingdom 1unstable0.32
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 1unstable0.30
3DGD - 3D Genome Database China 6unstable0.86
IEDB - The Immune Epitope Database United States 28alive3.96
NeuroPedia - Neuropeptide Database United States 15alive2.08
PathLocdb - Pathway Localization Database China 10unstable0.29
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
PhosphoNetworks United States 11alive2.75
3D-interologs - 3D-domain interactions based on homologous proteins
Taiwan 18alive2.25
SeqDepot
United States 1alive0.25
Sinbase - Sesamum indicum database China 14unstable4.15
HIPdb - Database of HIV inhibiting peptides India 19alive3.80
Plant-PrAS - Plant-Protein Annotation Suite Japan 4alive1.33
PolysacDB India 4alive0.67
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 30alive3.64
LipidHome - database of theoretical lipids optimized for high throughput mass spectrometry lipidomics
United Kingdom 20unstable3.24
SyStemCell China 6unstable0.74
YRC PIR - The Yeast Resource Center Public Image Repository United States 20alive2.47
WALTZ-DB - database of amyloid-forming peptides Belgium 0alive0.00
MCG - Maize Cell Genomics Database United States 4alive1.33
TassDB2 - TAndem Splice Site DataBase Germany 45alive4.05
MTTD - Medicago Truncatula Transporter database China 6unstable0.64
MUFOLD-DB - A Solution For Protein 3D Structure Prediction
United States 1unstable0.24
mpMoRFsDB - Database of Molecular Recognition Features in Membrane Proteins
Greece 6alive1.19
wDBTF - Inventory Database of Wheat Transcription Factor France 19unstable1.78
MPIC - Mitochondrial Protein Import Components Database Australia 5alive1.67
RedoxDB - protein oxidative modification database Hong Kong SAR China 25alive4.13
mUbiSiDa - Database of mammalian protein ubiquitination site China 14unstable3.33
TRIP - TRansient receptor potential channel-Interacting Protein
Korea Rep. 34alive4.76
TumorHoPe - Tumor Homing Peptide Database
India 29alive4.83
CoDNaS - Conformational Diversity of Native State
Argentina 19unstable1.75
RefProtDom - a protein database with improved domain boundaries and homology relationships. United States 6alive0.74
UniVIO - Uniformed Viewer for Integrative Omics Japan 13alive2.57
PrionHome Canada 9dead0.03
ProFITS - Protein Families Involved in the Transduction of Signalling China 7alive0.85
PupDB - database of pupylated proteins Taiwan 23alive3.80
dbGSH - databaseof cysteine S-glutathionylation (GSH) sites Taiwan 25alive6.19
dbTEU - DataBase of Trace Element Utilization United States 14unstable1.64
GPCR-RD - A Database For Experimental Restaints Of GPCRs United States 38alive4.75
DetoxiProt - An integrated database of detoxification proteins China 3unstable0.34
HSC-explorer - hematopoietic stem cell explorer Germany 6unstable1.07
CLIPdb China 0alive0.00
CyanoPhyChe India 2alive0.33
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 10alive1.24
footprintDB - footprintDB
Spain 9alive2.25
IRView - Database and viewer of interacting regions (IRs) in protein sequences Japan 1alive0.17
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.03
NMPdb - Database of Nuclear Matrix Proteins.
United States 53dead0.00
SPD - Secreted Protein Database China 119unstable5.22
eBLOCKs - eBLOCKs
United States 28dead0.00
PDBSITE Russian Federation 92alive7.01
ADDA
Finland 44dead0.00
FunShift
Sweden 44alive3.38
PRECISE - Predicted and Consensus Interaction Sites in Enzymes United States 16dead0.00
ProDom France 251alive19.31
S4
United Kingdom 20dead0.00
SBASE
Italy 23unstable1.03
SYSTERS
Germany 51unstable2.43
PDB-Ligand Korea Rep. 58unstable1.56
CSS - Carbohydrate Structure Suite
Germany 121dead0.00
GenDiS - Genomic Distribution of Protein Structural Domain Superfamilies India 16alive1.23
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343unstable22.16
STING Report
Brazil 22alive1.69
PFD - Protein Folding Database Australia 30unstable1.22
Integr8
United Kingdom 169unstable10.79
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive30.76
CYGD - Comprehensive Yeast Genome Database Germany 327unstable20.63
PROPHECY - PROfiling of PHEnotypic Characteristics in Yeast Sweden 29alive2.23
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive3.92
3D-footprint
Spain 34alive4.25
RegPrecise - Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes United States 141unstable16.22
TransmiR - TF–miRNA Regulatory Database
China 184alive23.00
MeMotif - A wiki for motifs in transmembrane proteins
Germany 15alive1.88
SuperCYP
Germany 102alive12.75
FunSimMat - Functional Similarity Matrix
Germany 87alive8.61
ComSin
Russian Federation 22alive2.67
fPOP - footprinting Pockets Of Proteins
United States 11dead0.00
PGD - Protein Geometry Database United States 19unstable1.73
PTGL - Protein Topology Graph Library Germany 10dead0.00
PNU - Protein Naming Utility United States 6unstable0.69
DynaProt 2D - Proteome Database of Lactococcus lactis Germany 15alive1.15
MetaRouter - Bioinformatics for Bioremediation United Kingdom 38alive2.89
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
AMPDB - Arabidopsis Mitochondrial Protein Database Australia 68alive5.23
MiST2 - Microbial Signal Transduction Database United States 147unstable15.43
FlyTF - Transcription factor datamine for Drosophila melanogaster United Kingdom 128unstable8.96
MetaBioME - Comprehensive Metagenomic BioMining Engine Japan 36alive4.45
UM-BBD - University of Minnesota Biocatalysis/Biodegradation Database United States 94dead0.00
CORUM - Comprehensive Resource of Mammalian protein complexes Germany 269alive32.62
DP - Dynamic Proteomics Israel 15dead0.00
GWIDD - Genome-wide Protein Docking Database
United States 30alive3.68
PepX - A structural database of non-redundant protein-peptide complexes Belgium 60alive7.50
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 105alive13.13
AtNoPDB - Arabidopsis Nucleolar Protein Database United Kingdom 61alive4.50
GeneFarm - GeneFarm France 22dead0.00
PeroxisomeDB - PEROXISOME database Spain 61alive7.55
PlnTFDB - Plant Transcription Factor Database Germany 246alive30.44
SALAD Japan 36alive4.37
AntigenDB
India 35unstable3.81
TRANSFAC - a database on transcription factors and their DNA binding sites Germany 7590unstable200.10
CyBase
Australia 220unstable8.98
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable10.65
REFOLD
Australia 81dead0.00
LOCATE - subcellular localization database Australia 87alive7.25
NOPdb - Nucleolar Proteome Database United Kingdom 96dead0.00
NURSA - Nuclear Receptor Signaling Atlas
United States 93alive7.75
PAZAR - A public database of transcription factor and regulatory sequence annotation Canada 65alive7.22
SitesBase
United Kingdom 91dead0.00
BIOZON
United States 53unstable3.93
MulPSSM - A Database of Multiple Position-specific Scoring Matrices of Protein Domain Families
India 28unstable0.49
SDR - Specificity-determining Residue Database
United States 16dead0.00
SuperSite
Germany 28unstable2.64
TMFunction
Japan 23dead0.00
Protein Clusters United States 160unstable8.00
Degradome - The Degradome database Spain 107dead0.00
Kinomer United Kingdom 49alive5.44
EROP - Endogenous Regulatory OligoPeptide knowledgebase
Russian Federation 41alive3.42
DMAPS - Database of Multiple Alignments for Protein Structures
United States 10dead0.00
FSN - Flexible Structural Neighborhood
United States 13alive1.08
iMOTdb - interacting Motif Database
India 3alive0.25
MolMovDB - Database of Macromolecular Movements
United States 652unstable29.01
PMDB - Protein Model Database Italy 194unstable2.42
OKCAM - Ontology for Cell Adhesion Molecules United States 10unstable1.03
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable162.49
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees United Kingdom 65unstable4.44
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.61
CC+
United Kingdom 78alive8.67
ConSurf-DB
Israel 104alive11.44
Circular Permutation Database
Taiwan 36alive3.96
GTOP - Genomes TO Protein Structures and Functions database Japan 26alive2.80
JAIL - Just another interface library
Germany 7alive0.78
KineticDB
Russian Federation 53unstable4.12
PiSite - Database of Protein Interaction Sites Japan 28alive3.11
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive8.33
RsiteDB - RNA binding site database
Israel 19alive2.11
SPROUTS - Structural Prediction for pRotein fOlding UTility System
United States 21dead0.00
Voronoia - Voronoia Germany 52alive5.78
VIPERdb - Virus Particle Explorer United States 293alive24.42
ARDB - Antibiotic Resistance Genes Database
United States 284alive31.24
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive3.78
Genolevures - Genomic Exploration of the Hemiascomycete Yeasts France 223unstable6.05
ExplorEnz - The Enzyme Database
Ireland 54alive6.00
Bionemo - Biodegradation Network Molecular Biology Database
Spain 15alive1.67
PMAP - The Proteolysis MAP United States 31unstable2.34
PIPs - human protein–protein interaction prediction database United Kingdom 114alive12.67
ExDom - ExDom United States 10unstable0.30
Pseudofam - pseudogene families database United States 20alive2.20
HPRD - Human Protein Reference Database India 3067unstable190.15
Human Proteinpedia India 65unstable6.72
CTdatabase - Cancer-Testis Database Brazil 116unstable12.12
MoKCa - Mutations, Oncogenes, Knowledge & Cancer United Kingdom 34alive3.74
AutDB - Autism Spectrum Disorders database United States 121unstable12.37
DNAReplication - DNAReplication United Kingdom 10alive1.08
Sys-BodyFluid China 57unstable1.39
APD - Antimicrobial Peptide Database United States 572alive62.28
GabiPD - GABI Primary Database Germany 36alive3.88
PhytAMP - antimicrobial plant peptides Tunisia 105unstable2.92
ProSAS - Protein Structure and Alternative Splicing database Germany 24unstable0.96
DBTBS - Database of Transcriptional Regulation in Bacillus subtilis Japan 495alive29.12
TAIR - The Arabidopsis Information Resource United States 768unstable52.22
PlantTribes United States 57unstable5.24
Mitome - A Database for Comparative Mitochondrial Genomics in Metazoan Animals
Korea Rep. 34alive3.40
LigASite
Belgium 57dead0.00
Bacteriome.org - Bacteriome.org Canada 46unstable2.53
BMRB - Biological Magnetic Resonance Data Bank
United States 635alive63.50
BioHealthBase United States 70unstable5.60
GenoList - An Integrated Environment for the Analysis of Microbial Genomes France 50unstable4.15
ToxoDB - Toxoplasma gondii database United States 381alive25.40
MALISAM - Manual Alignments For Structurally Analogous Motifs
United States 20alive1.98
MegaMotifbase - Structural Motifs in Protein Families and Superfamilies
India 24alive2.40
PPT-DB - protein property prediction and testing database Canada 15alive1.50
PairsDB - Pairs Database United Kingdom 17dead0.00
ChromDB - The chromatin database United States 72unstable4.61
DB-PABP - DB-PABP
United States 4dead0.00
NORINE - A Database of Nonribosomal Peptides
France 171unstable14.88
Telomerase Database - Telomerase Database
United States 94alive9.31
GDB:Structures - Glycoconjugate Data Bank:Structures
Japan 33alive3.30
Greglist - Database of G-quadruplex Regulated Genes China 43unstable2.97
QuadBase - QuadBase India 71unstable6.46
SGDB - Synthetic Gene Database
United States 26unstable0.97
PharmGED - Pharmacogenetic Effect Database Singapore 8dead0.00
MAPU - Max-Planck Unified proteome database Germany 53alive4.82
SynDB - Synapse protein DataBase
China 35unstable1.69
PROTCOM - Protein Complexes United States 53dead0.00
SNAPPI-DB - SNAPPI-DB
United Kingdom 60alive5.45
GeneSpeed - GeneSpeed database United States 10dead0.00
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
DOMINO - DOMINO
Italy 72unstable1.31
LMSD - LIPID MAPS Structure Database
United States 279alive25.36
CYCLONET - CYCLONET
Russian Federation 15alive1.36
CutDB
United States 84alive7.41
BindingDB - BindingDB
United States 706alive63.54
eSLDB - eSLDB Italy 45alive4.09
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.64
GeneTrees - A Phylogenomics Resource For Prokaryotes United States 11dead0.00
SISYPHUS - SISYPHUS
United Kingdom 72alive6.55
Defensins knowledgebase - Defensins knowledgebase
Singapore 81alive7.36
Sentra - Sentra United States 20dead0.00
TransportDB - TransportDB United States 298alive27.09
GlycoMapsDB - GlycoMapsDB Germany 46alive4.18
TMBETA-GENOME Japan 20dead0.00
T-DB - TOPOFIT-DB
United States 19dead0.00
euHCVdb - European HCV Database United States 118unstable3.97
INVHOGEN - INVertebrate HOmologous GENes Germany 5dead0.00
LEGER - Post-genome Database for Listeria Research Germany 24unstable1.24
MPact - MIPS Protein Interaction Resource on Yeast Germany 357unstable12.20
SGCEdb United States 2dead0.00
LMPD - LIPID MAPS Proteome Database
United States 43alive3.58
AffinDB - Affinity database for protein-ligand complexes
Germany 84alive7.00
pSTIING United Kingdom 47alive3.92
MfunGD - MIPS Mouse Functional Genome Database Germany 14unstable0.50
PepSeeker - A database of proteome peptide identifications for investigating fragmentation patterns United Kingdom 38dead0.00
PeptideAtlas United States 839alive69.22
ChloroplastDB - Chloroplast Genome Database United States 68unstable5.21
MitoP2 - An integrative tool for the analysis of the mitochondrial proteome Germany 156dead0.00
Epitome - Epitome
United States 58unstable3.58
NetworKIN - A Resource for Exploring Cellular Phosphorylation Networks Canada 195alive19.50
DisProt - Database of Protein Disorder United States 838alive63.82
COMBREX-DB - COMBREX database United States 0alive0.00
RBP-Var China 0alive0.00
PDBFlex United States 1alive0.50
SIB - Swiss Institute of Bioinformatics
Switzerland 6unstable1.25
BIGNASim - BIGNASim database structure and analysis portal for nucleic acids simulation data
Spain 1alive0.50
UET - Universal Evolutionary Trace United States 1alive0.49
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 1alive0.50
EBI - The European Bioinformatics Institute United Kingdom 610unstable21.10
CPPsite - Database of Cell-Penetrating Peptides
India 70alive11.67
iGNM - Gaussian Network Model Database United States 116alive8.92
HGTree - Database of Horizontally Transferred Genes Determined by Tree Reconciliation Pakistan 1alive0.48
EMDataBank - Unified Data Resource for 3-Dimensional Electron Microscopy
United States 1alive0.50
SugarBindDB - SugarBind Database Switzerland 10alive2.00
DBAASP - Database of Antimicrobial Activity and Structure of Peptides Georgia 9alive2.25
Start2Fold Belgium 1alive0.50
GEneSTATION United States 1alive0.49
NCBI - National Center for Biotechnology Information United States 16174unstable395.36
ONRLDB - Orphan Nuclear Receptor Ligand Binding Database
India 0alive0.00
ProPepper Hungary 0dead0.00
MicRhoDE - Microbial Rhodopsin database for Diversity and Evolution studies France 1unstable0.32
MetazSecKB - Metazoa (Human/Animal) Secretome and Subcellular Proteome KnowledgeBase United States 0alive0.00
EpiFactors - EpiFactors Russian Federation 3alive0.99
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 1unstable0.26
SATPdb - A database of structurally annotated therapeutic peptides
India 1alive0.50
RBCC - Red Blood Cell Collection Hungary 1alive0.33
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 0unstable0.00
JuncDB Israel 1alive0.50
READDB - RNA Binding Protein Expression and Disease Dynamics database
United States 0alive0.00
HCSD - Human Cancer Secretome Database Sweden 1unstable0.32
IID - Integrated interactions database Canada 1alive0.50
NBDB - Nucleotide binding database
Singapore 1alive0.50
BDB - Biopanning Data Bank
China 0unstable0.00
Colorectal Cancer Atlas Australia 1alive0.50
KLIFS Netherlands 2alive0.99
PDBe - Protein Data Bank in Europe United Kingdom 239alive29.88
iPPI-DB - Inhibitors of Protein–Protein Interaction Database
France 9alive4.50
SIDER - Side Effect Resource
Germany 2alive1.00
PlantPAN - Plant Promoter Analysis Navigator Taiwan 188alive18.80
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.49
GtoPdb - IUPHAR/BPS Guide to PHARMACOLOGY United Kingdom 2alive0.98
MitoCarta - An Inventory of Mammalian Mitochondrial Genes United States 2unstable0.65
HCVpro - Hepatitis C Virus Protein Interaction Database South Africa -unstable-
POSTAR - POST-trAnscriptional Regulation China 1alive0.96
ADPriboDB - The Database of ADP-ribosylated proteins United States 0alive0.00
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive1.33
LinkProt Poland 0alive0.00
Membranome - Membrane Proteome United States 1unstable0.70
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 94unstable1.18
ECOD - Evolutionary Classification of Protein Domains United States 33alive8.25
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 1unstable0.82
PX - ProteomeXchange
United Kingdom 1059unstable240.92
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 9alive1.25
HistoneDB - histone database
United States 4dead0.00
KinetochoreDB
Australia 0dead0.00
CCProf Taiwan 0alive0.00
UbiNet - Ubiquitylation Networks Taiwan 1alive0.49
CoopTFD - Cooperative Transcription Factors Database Taiwan 1alive0.48
Tfcheckpoint - Transcription Factor Checkpoint Norway 8alive1.60
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 1alive0.50
TOPDOM - database of conservatively located domains and motifs in proteins
Hungary 27alive2.70
* Citations derived from Google Scholar.
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