Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
NCBI Gene - NCBI Gene United States 1802unstable76.58
euL1db - European database of L1HS retrotransposon insertions in humans France 2unstable0.95
Islander - Database of Genomic Islands United States 4alive2.00
MethBank - Methylation Bank China 6alive3.00
APASdb - Alternative PolyAdenylation Sites Database China 4unstable1.68
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive12.00
AnimalTFDB - Animal Transcription Factors Database China 82alive15.91
COXPRESdb - Coexpression Database Japan 230alive25.56
DBTSS - DataBase of Transcriptional Start Sites Japan 767alive51.13
EPD - Eukaryotic Promoter Database Switzerland 32alive16.00
TFClass - Classification of Human Transcription Factors and Mouse Orthologs Germany 48unstable11.40
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive4.00
TTSMI - triplex target DNA site Mapping and Integration database Singapore 1alive0.50
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive45.38
RNAcentral United Kingdom 31alive15.04
Rfam - RNA Families
United Kingdom 3329alive237.79
The tmRNA website - The tmRNA website United States 300alive15.79
tRFdb - Transfer RNA related Fragments Database United States 4alive1.98
miRDB - miRNA target prediction and functional annotations database United States 465alive51.67
DIANA-TarBase - DIANA-TarBase Greece 1513alive137.55
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115alive22.77
lncRNAdb Australia 351alive57.91
LNCipedia - A comprehensive compendium of human long non-coding RNAs Belgium 168unstable32.76
lncRNASNP China 17alive8.33
LncRNAWiki - a wiki-based platform for community curation of human lncRNAs China 15unstable6.07
LncRNA2Target - LncRNA-target association database China 12unstable2.58
MeT-DB - The MethylTranscriptome DataBase China 3alive1.44
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
OrthoDB - Orthologs Database Switzerland 468alive52.00
SMART - Simple Modular Architecture Research Tool
Germany 3106alive161.84
COG - Clusters of Orthologous Genes United States 11125unstable289.25
MBGD - Microbial Genome Database Japan 279alive19.73
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
RCSB PDB - RCSB Protein Data Bank United States 853unstable122.26
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
Rhea
Switzerland 66alive13.20
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
PhosphoSitePlus United States 653alive130.60
ProteomeScout United States 0unstable0.00
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
P2CS - Prokaryotic 2-Component Systems France 80alive9.90
BioModels
United Kingdom 23alive11.50
CeCaFDB - Central Carbon Metabolic Flux Database China 0unstable0.00
Cfam - Chemical Families Database
Singapore 0dead0.00
HIV-1 Human Interaction Database United States 171unstable9.88
Viral Genomes - Viral Genomes United States 0unstable0.00
ViRBase - virus-host ncRna interaction database China 0alive0.00
VirHostNet - Virus-Host Network France 93unstable9.88
VirusMentha - VirusMentha Italy 0alive0.00
rrnDB - Ribosomal RNA Operons Database United States 988unstable17.91
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable54.86
GenoBase - Escherichia coli K-12 Resource Database Japan 5unstable1.15
MyMpn - The Mycoplasma pneumoniae database Spain 11unstable4.95
PAIDB - Pathogenicity Island Database Korea Rep. 110unstable7.79
DB-AT - Database of Apicomplexa Transcriptomes Germany 2alive1.00
TrypanoCyc - Trypanosoma brucei Database France 0alive0.00
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive30.60
PomBase United Kingdom 131alive26.20
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
FlyBase - Database of Drosophila Genes & Genomes United States 3836alive166.78
Helminth.net United States 12alive6.00
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable11.08
i5k Workspace@NAL United States 10alive5.00
iBeetle-Base - A database of Tribolium RNAi phenotypes Germany 0alive0.00
MGD - Mouse Genome Database United States 2658alive132.90
NHPRTR - Nonhuman Primate Reference Transcriptome Resource United States 31alive7.67
RGD - Rat Genome Database United States 60alive29.70
SuperFly Spain 0alive0.00
Xenbase - Xenopus model organism database Canada 214alive23.78
neXtProt - Exploring the universe of human proteins Switzerland 237unstable17.06
DBTMEE - Database of Transcriptome in Mouse Early Embryos Japan 2alive1.00
DoGSD - Dog Genome SNP Database China 5alive2.47
AFND - Allele Frequency Net Database United Kingdom 39alive9.75
OMIM - Online Mendelian Inheritance in Man United States 3217dead0.00
GRASP - Genome-Wide Repository of Associations between SNPs and Phenotypes United States 28unstable5.04
COSMIC - Catalogue of Somatic Mutations in Cancer United Kingdom 4018alive305.99
The UCSC Cancer Genomics Browser United States 187unstable6.78
MTB - Mouse Tumor Biology System United States 105alive6.56
arrayMap Switzerland 0unstable0.00
BCCTBbp - Breast Cancer Campaign Tissue Bank Bioinformatics Portal United Kingdom 3alive1.44
CancerPPD
India 0alive0.00
CCGD - Candidate Cancer Gene Database United States 8alive4.00
CMPD - Cancer Mutant Proteome Database Taiwan 0unstable0.00
Cancer3D United States 10alive4.95
MethHC - A database of DNA Methylation and gene expression in Human Cancer Taiwan 18alive8.91
YM500 - YM500 Taiwan 45alive11.14
VaDE - VarySysDB Disease Edition Japan 0alive0.00
DAA - Digital Ageing Atlas United Kingdom 9alive4.50
DDMGD - database of diseases associated gene methylation in different species Saudi Arabia 2unstable0.86
Dr.VIS - Viral integration sites China 14unstable2.13
EpilepsyGene - EpilepsyGene database China 3unstable1.35
Organ system heterogeneity DB - A Database for the Visualization of Phenotypes at the Organ System Level Germany 0alive0.00
ADReCS - Adverse Drug Reaction Classification System China 3unstable1.39
Open TG-GATEs - Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System Japan 17dead0.00
T3DB - The Toxin and Toxin Target Database Canada 73alive10.43
Super Natural II
Germany 11alive5.50
NutriChem - A Systems Chemical Biology Resource to Explore the Medicinal Value of Plant-based Foods. Denmark 2alive0.98
EHFPI - Database of Essential Host Factors for Pathogenic Infection
China 1unstable0.44
AHTPDB - Database of Antihypertensive Peptides India 7alive3.50
PubAngioGen China 0alive0.00
PLAZA - An online platform for plant comparative genomics Belgium 196unstable23.27
PNRD - Plant Non-coding RNA Database China 10unstable4.70
Plastid-LCGbase - The Plastid Lineage-based Conserved Gene-pair Database China 2unstable0.74
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana Korea Rep. 0alive0.00
Araport - Arabidopsis Information Portal United States 9unstable1.30
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
RiceVarMap - Rice Variation Map China 9alive4.45
SNP-Seek database - SNP-Seek Database Philippines 53unstable21.73
CGH - Coffee Genome Hub France 3alive1.50
SGN - Sol Genomics Network United States 0unstable0.00
Europe PMC - Europe PubMed Central
United Kingdom 43alive7.17
GO - Gene Ontology Consortium Switzerland 5117alive319.81
GOA database - Gene Ontology Annotation (UniProt-GOA) Database
United Kingdom 229alive44.88
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161alive20.13
DO - Disease Ontology United States 248alive49.10
HGNC - HUGO Gene Nomenclature Committee United Kingdom 612alive65.96
NCBI Taxonomy Database - NCBI Taxonomy Database
United States 13unstable3.38
diArk - Database for Eukaryotic Genome Research Germany 16alive1.60
ArrayExpress
United Kingdom 289alive70.81
CODEX
United Kingdom 13alive6.43
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive6.20
ImmuCo - a database of gene Co-expression and Correlation in Immune cells China 4unstable1.86
Cyclebase - Cell-cycle Database Denmark 105alive11.20
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.00
VCGDB - Virtual Chinese Genome Database China 1alive0.33
BioSamples
United Kingdom 39alive7.64
NGSmethDB - High-quality Methylation Maps Spain 52unstable5.20
uORFdb - upstream open reading frames database Germany 22unstable5.65
miRBase - microRNA dababase United Kingdom 11326alive853.81
miRNEST - miRNEST Poland 35alive6.93
miRTarBase - miRNA Target Database Taiwan 899alive149.83
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive26.14
starBase - starBase China 491unstable68.74
NONCODE - Noncoding RNAs China 637unstable47.77
NPInter - ncRNA Interaction Database China 119alive10.60
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive17.16
NDB - Nucleic Acid Database
United States 28alive9.15
RNA Bricks
Poland 20alive6.60
SMMRNA - Small Molecule Modulators of RNA
India 5alive1.67
JASPAR Canada 2924alive220.42
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive13.00
CollecTF - Database of Transcription Factor Binding Sites United States 31dead0.00
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
DPRP - Database of Phenotype-specific Regulatory Programs Taiwan 0alive0.00
Network portal - A Database for Storage, Analysis and Visualization of Biological Networks
United States 14alive4.67
KEGG - Kyoto Encyclopedia of Genes and Genomes Japan 25114alive1395.22
UniCarbKB - UniCarb KnowledgeBase Australia 85alive14.17
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
Laminin-database Brazil 4alive1.31
CentrosomeDB Spain 58alive7.11
SelenoDB
Germany 43alive4.78
Hemolytik - Database of Hemolytic peptides India 13alive4.33
CR Cistrome - Chromatin Regulator Cistrome China 6unstable1.64
MetaCyc database - A database describing metabolic pathways and enzymes from all domains of life.
United States 199unstable35.82
Reactome - A Curated Pathway Database United States 615alive205.00
SMPDB - The Small Molecule Pathway Database Canada 110alive15.40
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
Ensembl Genomes - Ensembl Genome Annotation System United Kingdom 293alive41.86
IMG - Integrated Microbial Genomes United States 568unstable30.67
DEG - Database of Essential Genes China 573alive44.08
PATRIC - Pathosystems Resource Integration Center United States 279unstable26.97
BacDive - Bacterial Diversity Metadatabase Germany 8alive2.67
EBI Metagenomics - EBI Metagenomics
United Kingdom 32unstable9.92
GGBN - Global Genome Biodiversity Network Germany 28alive9.24
LPSN - List of Prokaryotic names with standing in nomenclature United States 129alive43.00
MetaRef - A pan-genomic database for microbial genomics Italy 9alive2.88
POGO-DB - Database of Pairwise-comparisons Of Genomes and universal Orthologous genes United States 4alive1.33
RDP - Ribosomal Database Project United States 11954alive450.57
SILVA - High quality ribosomal RNA databases Germany 3927unstable137.44
COLOMBOS Belgium 35alive5.83
DOOR - Database of Prokaryotic Operons United States 218alive26.98
Virus Variation - Virus Variation United States 21unstable3.64
CyanoBase Japan 36alive12.00
RhizoBase Japan 19alive6.27
HoPaCI-DB - The Host-Pseudomonas and Coxiella Interaction database France 3unstable0.94
PortEco - potral for E. coli research United States 13alive4.16
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
CGD - Candida Genome Database United States 167alive33.07
SGD - Saccharomyces Genome Database United States 772alive154.40
LoQAtE - The localization and quantitation atlas of the yeast proteome Israel 8alive2.61
YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiae Korea Rep. 17alive5.67
BacMet - Antibacterial Biocide and Metal Resistance Genes Database Sweden 16unstable4.96
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
WormQTLHD - A Web Database for Linking Human Disease to Natural Variation Data in C. elegans. Netherlands 27alive6.75
IMPC - International Mouse Phenotyping Consortium United Kingdom 44alive14.52
GXD - The mouse Gene Expression Database United States 479alive23.95
MPD - Mouse Phenome Database United States 201unstable18.09
EMAGE - Mouse Embryo Spatial Gene Expression Database United Kingdom 234alive20.63
TISdb - translation initiation site database United States 16alive5.33
GeneProf - GeneProf United Kingdom 44unstable8.18
CCDS - Consensus Coding Sequence United States 394unstable14.28
LRG - Locus Reference Genomic United Kingdom 155alive22.14
ExoLocator - ExoLocator Singapore 5alive1.63
Manteia France 18alive6.00
AgeFactDB - Ageing Factor Database Germany 8alive2.67
PhylomeDB - Phylome DataBase Spain 241alive26.78
dbPSHP - Database of Positive Selection across Human Populations Hong Kong SAR China 16alive5.33
Selectome - A Database of Positive Selection Switzerland 43alive5.32
TreeFam - database of phylogenetic trees United Kingdom 529alive48.09
Expression Atlas - Expression Atlas United Kingdom 90alive28.80
GEISHA - Gallus Expression In Situ Hybridization Analysis United States 113alive8.34
The Gene Expression Barcode United States 15alive4.95
PED - Pancreatic Expression Database United Kingdom 75alive7.50
CellFinder Germany 5alive1.67
PPD - Plasma Proteome Database India 53unstable16.25
dbGaP - Database of Genotypes and Phenotypes United States 85unstable14.73
ClinVar - variation-phenotype relationships United States 944unstable163.63
DGV - Database of Genomic Variants Canada 233alive77.67
DECIPHER - Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. United Kingdom 41unstable3.96
NECTAR - Non-synonymous Enriched Coding muTation ARchive United Kingdom 0alive0.00
FINDbase - Frequency of Inherited Disorders Database Greece 111alive11.10
InvFEST - Human Polymorphic Inversion DataBase Spain 14alive4.67
rSNPBase - A Database for Curated Regulatory SNPs China 35alive11.67
canSAR United Kingdom 70unstable13.30
DriverDB - database for cancer driver gene/mutation Taiwan 18alive6.00
Progenetix Switzerland 179unstable10.40
HbVar - Human Hemoglobin Variants and Thalassemias United States 510alive39.23
HMDD - Human MicroRNA Disease Database China 61alive20.33
BioAssay
United States 84unstable14.56
ChEMBL
United Kingdom 1746unstable324.76
DrugBank - Open Data Drug and Drug Target Database
Canada 3839alive349.00
SuperPain Germany 3alive1.00
Transformer Germany 8alive2.67
TTD - Therapeutic target database Singapore 232alive45.47
VIOLIN - Vaccine investigation and online information network United States 20alive6.67
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22alive7.33
SAbDab - The Structural Antibody Database United Kingdom 23unstable6.52
AVPdb
India 16alive5.33
CAMP - Collection of Anti-Microbial Peptides
India 218alive30.52
GoMapMan - GoMapMan Slovenia 16alive5.33
P-MITE - Plant Miniature Inverted Transposable Element database China 24alive7.76
PlantTFDB - Plant Transcription Factor Database China 684unstable45.60
ppdb - plantpromoterdb Japan 19alive6.33
Gramene - A comparative resource for plants United States 79alive26.33
LSD - Leaf Senescence DataBase China 42unstable6.16
P3DB - Plant Protein Phosphorylation DataBase United States 129alive16.13
RiceWiki China 7alive2.31
CottonGen United States 42alive14.00
GDR - Genome Database for Rosaceae United States 343unstable24.54
SoyKB - Soybean Knowledge Base United States 26alive8.49
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive1.32
ENCODE - Encyclopedia of DNA Elements United States 2053unstable45.80
Dfam - Dfam United States 58unstable9.57
SINEBase - A Database and Tools for SINE Analysis Russian Federation 27alive6.68
DoriC - Database of oriC regions in Bacterial and Archaeal genomes China 111unstable10.43
Non-B DB - A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs United States 68dead0.00
UCNEbase - A database of ultraconserved non-coding elements and genomic regulatiory blocks Switzerland 20alive5.00
APPRIS - Annotating Principal Splice Isoforms Spain 39alive9.75
HEXEvent - Human EXon splicing Events database United States 14alive3.36
SpliceAid-F Italy 20dead0.00
Spliceosome Database United States 20alive4.85
GeneTack database - GeneTack database United States 6dead0.00
Factorbook - Factorbook United States 61unstable4.27
ChIPBase China 199unstable30.35
CTCFBSDB - CTCF Binding Sites and Genome Organization Database United States 118alive12.98
HOCOMOCO - Homo Sapiens Comprehensive Model Collection Russian Federation 62alive15.50
SwissRegulon - A Database of Genome-wide Annotations of Regulatory Sites Switzerland 118unstable8.61
NCBI Epigenomics - NCBI Epigenomics United States 51unstable2.55
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive6.62
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable20.58
miRGator - miRGator Korea Rep. 228alive24.32
Darned - DAtabase of RNa EDiting Ireland 128alive18.10
MODOMICS - A Database of RNA Modifications Poland 509alive45.81
RNApathwaysDB - RNA Pathways Database Poland 5alive1.24
PlantRNA France 13alive3.12
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
KEGG OC - KEGG Ortholog Cluster Japan 37alive9.25
OrtholugeDB - A Bacterial and Archaeal Orthology Resource Canada 17alive4.21
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive213.50
TIGRFAMs - TIGR defined protein families
United States 940unstable53.46
The Genome Properties database - The Genome Properties database United States 65unstable14.79
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
KIDFamMap - Kinase-inhibitor-disease family map Taiwan 6alive1.50
PeroxiBase France 333alive30.27
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive5.50
ZiFDB - Zinc Finger Database United States 73dead0.00
ChEBI - Chemical Entities of Biological Interest
United Kingdom 187alive46.75
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
dcGO - Database of Domain-centric Ontologies
United Kingdom 30alive7.50
Genenames.org - HGNC Genenames.org United Kingdom 785alive84.61
DGA - Database of Disease and Gene Annotations China 23alive5.75
BioGPS
United States 99alive24.75
MyGene.info - Gene Annotation Query as a Service
United States 99alive24.75
HBVdb - Hepatitis B Virus database France 16unstable1.16
PaVE - PapillomaVirus Episteme United States 83unstable8.72
ViralZone - ViralZone Switzerland 76alive12.67
PR2 - Protist Ribosomal Reference Database France 80alive20.00
EcoCyc - BioCyc Database Collection United States 3517unstable90.44
EcoGene - The EcoGene Database of Escherichia coli Sequence and Function United States 312unstable16.15
ECMDB - Escherichia coli Metabolome Database Canada 32alive8.00
MicroScope - Microbial Genome Annotation & Analysis Platform France 195alive48.26
metaMicrobesOnline - Phylogenomic Analysis of Microbial Communities United States 5alive1.24
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive5.94
SecReT4 - Type IV Secretion System Resource China 21unstable4.88
SEVA - Standard European Vector Architecture Spain 87alive21.75
dictyBase - Database for Dictyostelium Discoideum United States 128alive16.00
EuPathDB - The Eukaryotic Pathogen database United States 168alive23.76
GenColors - GenColors Germany 17alive1.40
LAMP - Library of Apicomplexan Metabolic Pathways United Kingdom 19alive4.75
CFGP - Comparative Fungal Genomics Platform Korea Rep. 102unstable7.59
NetwoRx - Connecting Drugs to Networks and Phenotypes in Saccharomyces Cerevisiae Canada 6alive1.49
SchistoDB - Schistosoma Genomic Resources Brazil 94alive11.63
WDDD - Worm Developmental Dynamics Database Japan 4alive1.00
FlyAtlas - Drosophila gene expression atlas United Kingdom 983alive98.30
MonarchBase - The Monarch Butterfly Genome Database United States 23unstable5.41
enzyme portal - enzyme portal
United Kingdom 13alive3.25
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161alive30.91
WholeCellKB - WholeCellKB United States 16alive4.00
CPDB - Consensus Pathway Database Germany 368unstable25.30
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
OikoBase - A curated genome expression database of Oikopleura dioica Norway 16unstable3.76
ZFIN - Zebrafish Information Network United States 899alive44.50
ZInC - Zebrafish Insertional Collection United States 15unstable1.95
QTLdb - Animal QTL database United States 143unstable31.10
H2DB - Heritability Database Annotating with Trait-Associated Genomic Loci Japan 1alive0.25
RhesusBase China 12unstable2.79
H-InvDB - H-Invitational Database Japan 109alive12.11
Atlas of Genetics and Cytogenetics in Oncology and Haematology - Atlas of Genetics and Cytogenetics in Oncology and Haematology France 1188alive69.88
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable4.29
dbVar - Database of Genomic Structural Variation United States 41unstable5.33
DGVa - The Database of Genomic Variants archive
United Kingdom 41alive10.05
CellLineNavigator Germany 9alive2.25
GDSC - Genomics of Drug Sensitivity in Cancer United Kingdom 114alive28.22
TP53 mutation database France 30unstable5.63
TSGene - tumor suppressor gene database United States 89unstable5.78
SomamiR United States 27alive6.68
LncRNADisease - Database on lncRNA-disease associations China 267unstable49.40
GEO - Gene Expression Omnibus United States 9384unstable325.31
Allen Brain Atlas United States 67alive16.75
CircaDB - Circadian Database United States 61unstable8.54
GenomeRNAi - A Database for Cell-based and In Vivo RNAi Phenotypes Germany 45alive11.03
HAGR - Human Ageing Genomic Resources United Kingdom 595alive49.58
HemaExplorer Denmark 49unstable9.21
INTERFEROME Australia 224alive27.44
METscout - METscout
Germany 2alive0.50
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
PRIDE - PRoteomics IDEntifications United Kingdom 846alive205.15
Clone DB
United States 6unstable0.78
LUCApedia - Last Universal Common Ancestor United States 10unstable2.38
IUPHAR-DB United Kingdom 144alive23.52
TCMID - Traditional Chinese Medicines Integrated Database
China 53alive12.72
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
StreptomeDB Germany 28alive6.86
SwissBioisostere - A Database of Molecular Replacements for Ligand Design
Switzerland 30alive7.43
MIPS PlantsDB - Plant Genome and Systems Biology Germany 43alive10.75
PGDD - PLANT GENOME DUPLICATION DATABASE United States 97alive24.01
PIECE - Plant Intron Exon Comparison and Evolution database United States 27unstable3.91
PRGdb Italy 98unstable4.34
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
RGKbase - Rice Genome Knowledgebase China 9unstable1.66
RiceXPro - Rice Expression Profile Database Japan 189alive30.56
RiceFREND - Rice Functionally Related Gene Expression Network Database Japan 29alive7.03
IMGT/HLA United Kingdom 370alive90.65
InnateDB Canada 339unstable30.89
CIL-CCDB - Cell Image Library United States 14alive3.47
NCBI Bookshelf - NCBI Bookshelf United States 8unstable1.04
DOR - DDBJ Omics Archive
Japan 35alive6.93
DDBJ BioProject - The DNA Data Bank of Japan BioProject
Japan 35alive6.93
SRA - Sequence Read Archive United States -unstable-
GeneDB - GeneDB United Kingdom 92alive18.22
IMG/M - Integrated Microbial Genomes and Metagenomes United States 605unstable19.49
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable9.18
ScerTF - Saccharomyces cerevisia Transcription Factors Database United States 35unstable4.06
YeTFaSCo - Yeast Transcription Factor Specificity Compendium Canada 31alive6.20
DBG2I - Database for bacterial group II introns Canada 37unstable4.51
mirEX - MicroRNA Expression Database Poland 16unstable2.34
NAPP - Nucleic Acids Phylogenetic Profiling France 8unstable1.47
VIRsiRNAdb - database of viral siRNA/shRNA India 17alive3.40
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
Histome - The Histone Infobase India 49unstable9.11
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
Polbase - Polymerase Database United States 8unstable0.46
ProGlycProt - Prokaryotic Glycoproteins India 13alive2.52
ProRepeat Netherlands 10unstable0.50
BitterDB
Israel 57alive11.40
COD - Crystallography Open Database
Lithuania 263alive32.55
SCRIPDB
Canada 7alive1.39
MINAS - Metal Ions in Nucleic Acids
Switzerland 15alive3.00
RNA CoSSMos - RNA Characterization of Secondary Structure Motifs Database
United States 18alive3.60
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
GOLD - Genomes On Line Database United States 1646unstable43.39
Identifiers.org
United Kingdom 97alive19.40
MIRIAM Registry - MIRIAM Registry
United Kingdom 97alive19.01
HFV - Hemorrhagic Fever Viruses (HFV) Database United States 9alive1.78
ViPR - virus pathogene resourse United States 57alive11.40
BacMap Canada 47alive3.92
BµG@Sbase United Kingdom 5alive0.33
CoryneRegNet - Corynebacterial Transcription Factors and Gene Regulatory Networks Germany 202unstable12.30
DBETH - Database of Bacterial ExoToxins India 20alive3.84
ICEberg - ICEberg is a web-based resource for integrative and conjugative elements found in Bacteria. China 52unstable9.57
ProOpDB - Prokaryotic Operon DataBase Mexico 61alive11.96
ProPortal - Prochlorococcus Portal United States 18alive3.56
VFDB - Virulence Factor Database China 448alive37.33
CADRE - Central Aspergillus Resource United Kingdom 92unstable6.72
FungiDB - FungiDB United States 47alive9.40
OriDB - DNA Replication Origin Database United Kingdom 159alive15.90
PhenoM - Phenomics of yeast Mutants Canada 196unstable25.76
FlyRNAi - Drosophila RNAi screening center database United States 104unstable8.89
Nematode - Nematode.net United States 163alive12.54
UniPathway - UniPathway Switzerland 54unstable6.91
eQuilibrator - Biochemical Thermodynamics Calculator
Israel 65alive12.87
FunTree - FunTree
United Kingdom 23alive4.46
MACiE - Mechanism, Annotation and Classification in Enzymes
United Kingdom 45alive8.64
SABIO-RK
Germany 128alive12.80
hiPathDB - human integrated Pathway DB with facile visualization Korea Rep. 24alive4.80
IPAVS - Integrated Pathway Resources,Analysis and Visualization System
Korea Rep. 11unstable1.83
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive3.40
YMDB - Yeast Metabolome Database Canada 88alive17.60
HotRegion Turkey 23alive4.60
IBIS - Inferred Biomolecular Interactions Server
United States 33alive6.60
IntAct United Kingdom 499alive97.80
InterEvol
France 15alive2.97
MINT - Molecular Interaction Database
Italy 312unstable56.78
PINA - Protein Interaction Network Analysis Australia 281unstable23.53
Predictive networks United States 24unstable4.18
Newt-omics - A Comprehensive Repository for Omics Data from the Newt notophthalmus viridescens Germany 20alive4.00
OGEE - Online GEne Essentiality database China 77alive15.40
zfishbook - zebrafish book United States 3alive0.59
HGPD - Human Gene and Protein Database Japan 36alive4.50
HaploReg United States 457unstable85.92
SNPeffect - Single Nucleotide Variants Belgium 261alive21.75
DPSC-Cancer - Donnelly - Princess Margaret Screening Centre Cancer Database Canada 24alive4.75
dbDEPC - Database of Differentially Expressed Proteins in Human Cancer China 22unstable2.95
IGDB.NSCLC - Integrated Genomic Database of Non-Small Cell Lung Carcinoma Taiwan 10alive1.98
NCG - Network of Cancer Genes Italy 51alive10.20
SCDE - Stem Cell Discovery Engine United States 23alive4.60
UMD-BRCA1/BRCA2 - Universal mutation database-BRCA1/BRCA2 France 23dead0.00
ADHDgene - Database for Attention Deficit Hyperactivity Disorder China 27alive5.40
ALFRED - The ALlele FREquency Database United States 74unstable2.32
AutismKB China 74unstable8.88
BGMUT - Blood Group Antigen Gene Mutation Database United States 43unstable4.47
DiseaseMeth - Human Disease Methylation Database China 56alive10.75
DistiLD - Database of Diseases and Traits in Linkage Disequilibrium Denmark 17alive3.40
GWASdb - GWASdb Hong Kong SAR China 82alive16.40
SpliceDisease China 27dead0.00
GeneSigDB - Gene Signature DataBase United States 123unstable14.41
GeneWeaver - GeneWeaver United States 54alive10.80
modMine - A Data Warehouse for the modENCODE Project United Kingdom 50unstable9.00
RecountDB - A Database of Mapped and Count Corrected Transcribed Sequences
Japan 1dead0.00
DAMPD - Dragon Antimicrobial Peptide Database South Africa 39unstable4.91
SuperTarget
Germany 273unstable10.31
TDR - Tropical Disease Research Argentina 43unstable7.83
OligoGenome - Stanford Human Oligo Genome Project United States 3unstable0.47
PrimerBank United States 1063unstable65.30
HmtDB - Human Mitochondrial DataBase Italy 99unstable5.61
MitoMiner - A database of the mitochondrial proteome
United Kingdom 97alive12.00
MitoZoa - MitoZoa Italy 66dead0.00
MetaCrop - Metabolic pathways in crop plants Germany 73alive8.03
Phytozome - The Plant Genomics Resource United States 746unstable43.27
PlantNATsDB - Plant Natural Antisense Transcripts Database China 23alive4.51
PLEXdb - Plant Expression Database United States 136alive27.20
GABI-Kat SimpleSearch - GABI-Kat SimpleSearch Germany 206alive14.71
Plantmetabolomics.org United States 86unstable6.88
LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes United States 27alive5.18
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
MethylomeDB - database containing genome-wide brain DNA methylation profiles United States 33unstable2.90
MetaBase - Meta Database
Korea Rep. 21alive4.20
Gene Wiki - Gene Wiki United States 113unstable4.68
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable1.77
EcoliWiki - EcoliWiki United States 24unstable4.42
Xanthusbase - Myxococcus xanthus databse United States 16unstable0.56
959 Nematode Genomes United Kingdom 47unstable8.46
WikiPathways - WikiPathways Netherlands 228unstable30.10
SNPedia United States 67unstable11.26
SEQanswers wiki
China 21alive4.07
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.69
KGVDB Korea Rep. 4dead0.04
AREsite - AU-rich Elements Site Austria 110alive18.15
GyDB - The Gypsy Database Spain 127alive13.83
ASPicDB - Alternative Splicing Database
Italy 75dead0.00
DBASS - Databases of Aberrant 3'-ss and 5'-ss in Human Disease Genes Italy 19alive3.17
MPromDb - Mammalian Promoter Database United States 79dead0.00
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36unstable5.70
FlyFactorSurvey - Database of DNA binding specificities for Drosophila transcription factors (TFs) United States 78alive13.00
REDfly - Regulatory Element Database for Drosophila United States 284alive25.56
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive5.39
mESAdb - microRNA sequence and expression database Turkey 18alive3.00
PmiRKB - Plant microRNA Knowledge Base China 19alive3.10
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable5.12
RNAMDB - RNA Modification Database United States 1297unstable32.71
tRNADB-CE - The tRNA Gene DataBase Curated manually by experts
Japan 69alive8.54
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable3.03
PSORTdb Canada 191unstable13.37
CLIPZ - Cross-linking and Immunoprecipitation
Switzerland 72unstable9.72
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
RNA helicase database United States 30alive5.00
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
GlycomeDB - A Carbohydrate Structure Metadatabase
United States 122alive13.42
SuperSweet - Sweetening Agents Database
Germany 18alive3.00
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
AgBase United States 301alive27.36
BTO - BRENDA Tissue Ontology Germany 49alive8.09
IGRhCellID - Integrated Genomic Resources of Human Cell Lines for Identification Taiwan 2alive0.33
SCLD - Stem Cell Lineage Database United States 4unstable0.07
PRO - Protein Ontology United States 163alive26.62
CAMERA United States 257alive41.98
ODB - Operon DataBase Japan 79alive9.88
PhEVER - phylogenetic exploration of virues' evolutionary relationships France 4unstable0.11
Effective - Effective Germany 48alive7.92
Pseudomonas Genome DB Canada 565alive70.63
PSSRdb - Polymorphic Simple Sequence Repeats database India 6unstable0.64
TADB - Toxin-antitoxin Data Base China 94unstable14.41
AmoebaDB - Amoeba Genome Resource United States 35alive5.83
MicrosporidiaDB - Microsporidia Genomics Resource United States 35alive5.83
Full-parasites - Full-parasites Indonesia 13alive2.17
ParameciumDB - Paramecium Database France 128alive12.80
FGDB - Fusarium graminearum Genome Databas Germany 128unstable9.31
CiF - Cyber-infrastructure for Fusarium United States 40alive6.60
YPA - Yeast Promoter Atlas Taiwan 25unstable3.21
ArachnoServer - ArachnoServer Australia 131dead0.00
HGD - The Hymenoptera Genome Database United States 121alive19.76
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive6.00
Pathway Commons - Search and visualize public biological pathway information United States 395alive65.83
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
SPIKE - Signaling Pathways Integrated Knowledge Engine Israel 38alive6.33
CIPRO - Ciona Intestinalis Protein Database Japan 25alive4.17
cBARBEL - Catfish Genome Database United States 26unstable1.43
BGD - Bovine Genome Database United States 42alive5.88
IKMC - The International Knockout Mouse Consortium United States 62unstable4.65
FANTOM - Functional and taxonomic analysis of metagenomes Japan 144alive9.50
RIKEN Japan 28unstable1.07
TIARA - Total Integrated Archive of Short-Read and Array database Korea Rep. 15alive2.48
DAnCER - Disease Annotated Chromatin Epigenetics Resource Canada 17alive2.78
dbCRID - Chromosomal Rearrangements In Diseases United States 23unstable0.35
dbDNV - DNV Database Taiwan 11unstable1.45
IGDD India 13unstable1.69
VnD - Variations and Drugs Korea Rep. 7dead0.00
CancerResource Germany 59alive9.73
CaSNP China 17unstable2.30
CCDB - Cervical Cancer Gene Database India 42alive7.00
DDPC - Dragon Database of Genes associated with Prostate Cancer South Africa 26unstable4.03
The Autophagy Database Japan 25dead0.00
CADgene - Coronary Artery Disease Gene Database China 42unstable6.30
T1DBase - type 1 diabetes susceptibility Base United Kingdom 178unstable6.97
CPLM - Compendium of Protein Lysine Modifications
China 27unstable1.22
EDULISS - EDinburgh University Ligand Selection System
United Kingdom 17unstable1.02
FragmentStore - FragmentStore
Germany 11alive1.83
HIT - Herbal Ingredients' Targets Database China 60unstable7.40
PROMISCUOUS Germany 109alive18.17
Protegen - Protective Antigens United States 28unstable4.06
MitoGenesisDB - Mitochondrial Spatio-Temporal Expression Database France 3alive0.50
GreenPhylDB - GreenPhylDB France 130unstable4.33
NIASGBdb - NIAS Genebank database Japan 14alive2.31
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701alive50.07
AHD2 - Arabidopsis Hormone Database 2.0 China 60unstable4.05
AtPID - Arabidopsis thaliana Protein Interactome Database China 136alive14.51
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.17
TFGD - Tomato Functional Genomics Database United States 46alive7.67
iRefWeb - Literature curation of protein interactions
Canada 66alive7.19
GATMD - GABA Transporter Mutagenesis Database United States 7dead0.00
Pigment_Cell United States 3unstable0.22
EuroDia - EuroDia MicroArray Database Switzerland 9dead0.00
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.98
HOMD - The Human Oral Microbiome Database United States 216alive30.86
Shewanella knowledgebase United States 12dead0.00
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.86
MRB - Mouse Resource Browser Greece 3alive0.43
PDBWiki Germany 24alive3.43
CGDSNPdb - Center for Genome Dynamics Single Nucleotide Polymorphism Database United States 7dead0.00
BrainTrap - Fly Brain Protein Trap Database United Kingdom 14alive1.96
TRedD - Tandem Repeats Database United States 12unstable0.38
OpenFluDB - A Database for Human and Animal Influenza Virus Switzerland 17alive2.43
GOOD - Gene-Oriented Ortholog Database Taiwan 3unstable0.34
PhosphoGRID Canada 63unstable4.32
Bookshelf
United Kingdom 5alive0.71
Varietas - Varietas Finland 8dead0.00
AthaMap - Arabidopsis thaliana Map Germany 275alive20.94
GermOnline - GermOnline France 63unstable4.36
GeneCards - GeneCards Israel 900unstable29.37
HyperCAT Norway 20alive2.77
RAC - Repository of Antibiotic Australia 15dead0.00
hUbiquitome - ubiquitination cascades in humans China 14dead0.00
CPGR - Comprehensive Phytopathogen Genomics Resource United States 10alive1.67
INOH Japan 13dead0.00
SalmonDB - A Database for salmonids species Chile 14alive2.24
CELLPEDIA Japan 10alive1.67
Reactome BioMart - Reactome BioMart United Kingdom 8dead0.00
NetSlim - High-confidence Curated Signaling Maps
United States 18unstable2.73
BioMart
Canada 49alive7.84
Neisseria Base - A Comparative Genomics Database for Neisseria Meningitidis United States 5dead0.00
ICGC - International Cancer Genome Consortium Data Portal Canada 80dead0.00
SigReannot-mart France 7alive1.16
GETPrime - Gene and Transcript-specific Primer Database Switzerland 28alive4.62
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive3.00
The strategies WDK United States 9alive1.49
hERGAPDbase Japan 5unstable0.45
TparvaDB - Theileria parva vaccine development Database Kenya 2dead0.00
Allie - A Search Service for Abbreviation / Long Form
Japan 13alive2.17
LccED - The Laccase Engineering Database
Germany 42dead0.00
FunSecKB - Fungal Secretome KnowledgeBase United States 56alive9.24
the CEREALAB database - Cereals genotypic phenotypic source Italy 16unstable1.81
LPS-annotate Canada 8dead0.03
QlicRice - QTL and Loci Interaction Channels in Rice India 6unstable0.37
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.33
ParkDB - Parkinson's disease gene expression database United Kingdom 18dead0.00
Histone Database - Histone Database United States 19unstable0.89
CTD - Comparative Toxicogenomics Database United States 1016alive72.57
eFIP - eFIPonline
United States 13alive2.55
PubTator
United States 87unstable9.05
DFVF - Database of Known Fungal Virulence Factors United States 5alive0.99
The Units Ontology
United Kingdom 16dead0.00
CreZOO - CreZOO Greece 4unstable0.43
MuteinDB - The Mutein Database
Austria 4dead0.00
PRINTS - A compendium of protein fingerprints United Kingdom 42alive8.15
GrameneMart - BioMart data portal for the Gramene project United States 16alive3.20
The gene-specific codon counting database - The gene-specific codon counting database United States 8dead0.00
dbPTB - Database for Preterm Birth United States 16alive3.20
BFGR - Biofuel Feedstock Genomics Resource United States 12alive2.40
YeastMine - YeastMine United States 54alive10.80
Argo
United Kingdom 62unstable7.07
TGD Wiki - Tetrahymena genome database Wiki United States 8alive1.60
Aptamer base - Aptamer database
Canada 21unstable1.22
MEDIC - CTD's MEDIC disease vocabulary United States 54alive10.80
AntiFam
United Kingdom 10dead0.00
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.31
RefPrimeCouch - A Reference Gene Primer CouchApp Germany 1unstable0.17
wwpdb - worldwide protein data bank archive
United States 8alive1.98
CoIN - Co-occurrence Interaction Nexus
Taiwan 2dead0.00
HypoxiaDB - Hypoxia regulated proteins database India 3alive0.74
Tripal
United States 6alive1.50
RAvariome - Rheumatoid Arthritis Genetic Variants Database Japan 4alive1.00
HTS-DB - High-Throughput Screening DataBase United Kingdom 0alive0.00
yApoptosis - yeast apoptosis database Sweden 1alive0.25
BioC
United States 50alive12.25
IQdb - IQ genetic database China 8unstable0.34
metabolicMine - metabolicMine United Kingdom 10dead0.00
BGDB - Bivalent Genes Database China 4unstable0.07
BmTEdb - Bombyx mori Transposable Elements Database China 10unstable2.38
lncRNome - long noncoding RNA knowledgebase India 37unstable8.79
ESCAPE - Embryonic Stem Cell Atlas from Pluripotency Evidence United States 23alive5.75
CARLSBAD United States 5alive1.23
The Banana Genome Hub France 19alive4.75
RiceSRTFDB - Rice Stress-Responsive Transcription Factor Database India 9alive2.20
PhenoDigm - PHENOtype comparisons for DIsease and Gene Models United Kingdom 44alive10.89
PCorral - Protein Corral
United Kingdom 6unstable0.31
PMP - Protein Model Portal Switzerland 43alive10.75
hLGDB - The Human lysosome Gene Database Italy 6alive1.49
Variome - Variome Japan 4unstable0.66
MalaCards - The Human Disease Database Israel 97unstable14.79
curatedOvarianData United States 30unstable7.05
YY1TargetDB - Yin Yang 1 Target loci Database Hong Kong SAR China 3alive0.75
T-HOD - Text-mined Hypertension, Obesity and Diabetes candidate gene database Taiwan 9unstable2.12
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.58
PPInterFinder - Protein-Protein Interactions Finder India 17unstable0.38
Nencki Genomics Database - Ensembl Funcgen Enhanced With Intersections, User Data and Genome-wide TFBS Motifs. Poland 5alive1.23
BBGRE - Brain & Body Genetic Resource Exchange United Kingdom 2unstable0.03
SUS-BAR - Statistically Validated Annotation of Sus Scrofa Protein Sequences Italy 2unstable0.41
GnpIS - Genetic and Genomic Information System France 9unstable0.72
CREDO
United Kingdom 11alive2.64
MisPred - Miss Predict Protein Database Hungary 5unstable1.05
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.62
CHD@ZJU - Coronary Heart Disease Research Platform China 7unstable0.72
GoSynthetic - Synthetic Biology Workbench Germany 2alive0.50
eFG - Electronic Resource for Fusarium Graminearum China 1alive0.25
FSRD - Fungal Stress Response Database Hungary 8alive1.98
dbWFA - Database of Wheat Functional Annotation France 2unstable0.16
Eimeria TDB - The Eimeria Transcript DB Brazil 3alive0.75
pseudoMap Taiwan 10alive2.50
PIPEMicroDB - PIgeonPEa Microsatellite DataBase India 5dead0.00
bc-GenExMiner - Breast Cancer Gene-Expression Miner France 13alive3.25
dbPPT - Database of Protein Phosphorylation in Plants China 5alive1.67
EssOilDB - ESSential OIL DataBase India 4unstable1.16
HGV&TB - Database for Human Genes and Genetic Variants associated with Tuberculosis India 0unstable0.00
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
piRBase - piRNA database China 6unstable1.86
ChloroSSRdb - Chloroplastic Simple Sequence Repeats Database India 5unstable1.25
VIRmiRNA - Resource for experimental viral miRNA and their targets India 7alive2.33
PolyprOnline France 2unstable0.63
MelGene - Field Synopsis of Genetic Association Studies in Cutaneous Melanoma Greece 4unstable1.16
BactPepDB - Bacteria Peptide Database France 3alive0.98
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable1.24
MetaProx - The Database of Metagenomic Proximons Canada 2alive0.67
CanvasDB
Sweden 4alive1.33
CarrotDB China 14unstable3.87
CGHub - Cancer Genomics Hub United States 26unstable2.51
RGED - Renal Gene Expression Database China 1alive0.33
RADB - A Database of Rheumatoid Arthritis Related Polymorphisms China 1alive0.33
GOCat4FT - Gene Ontology Categorizer
Switzerland 2unstable0.61
LiverCancerMarkerRIF Taiwan 2unstable0.56
miRBase Tracker - miRBase Tracker Belgium 14unstable4.25
FusoBase - online Fusobacterium comparative genomic analysis platform Malaysia 0unstable0.00
Mouse IDGenes - Gene interactions in the developing mouse brain Germany 1alive0.33
LeishMicrosatDB - Database of leishmania genomic sequence repeats India 2unstable0.63
RLIMS-P - A Rule-based Literature Mining System for Protein Phosphorylation
United States 8alive2.67
BioCreAtIvE - Critical Assessment of Information Extraction systems in Biology
United States 2832alive236.00
tmBioC - text-mining BioC
United States 2unstable0.35
APADB Germany 8alive2.64
RTeQTL - Real-Time Online Engine for Expression Quantitative Trait Loci
United States 1unstable0.28
yStreX - Yeast stress expression database Sweden 2alive0.67
IFIM - Integrated Fitness Information for Microbial genes China 4unstable1.15
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.62
RegulonDB - Regulon DataBase Mexico 2506alive131.89
PhenotypeAnnotation Spain 4alive1.33
Osteosarcoma Database - An Osteosarcoma-gene Association Database Germany 4alive1.32
PTM-SD - Post Translational Modification Structural Database France 6alive2.00
iSimp - A Sentence Simplification System for Biomedical Text
United States 2alive0.65
HeteroGenome Russian Federation 2unstable0.63
dbCRY - Cryptochrome Database
Korea Rep. 2unstable0.49
TuberQ Argentina 7unstable1.73
FixPred - FixPred
Hungary 1unstable0.28
PhylOPDb - phylogenetic oligonucleotide probe database France 24unstable4.13
tagtog - tagtog United Kingdom 4alive1.33
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.73
DBatVir - the Database of Bat-Associated Viruses China 5alive1.67
YTRP - Yeast Transcriptional Regulatory Pathway Taiwan 5alive1.63
BambooGDB - Bamboo Genome Database China 12unstable2.84
ALE-HSA21 - AnaLysis of Expression of HSA21 Italy 5alive1.67
TSLP signaling pathway map - Thymic stromal lymphopoietin signaling pathway map United States 10unstable3.10
NONATObase - A Database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean Brazil 3unstable0.89
RegaDB - Rega database South Africa 2unstable0.44
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.58
tbvar - Mycobacterium tuberculosis variome resource India 5unstable1.58
Kin-Driver Argentina 7unstable2.19
iPathDB - INSECT PATHWAY DATABASE China