Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive4.00
CDD - Conserved Domain Database
United States 4407unstable269.93
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive60.39
KnotProt - A database of proteins with knots and slipknots
Poland 67alive13.40
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable3.72
RCSB PDB - RCSB Protein Data Bank United States 853unstable113.73
CATH
United Kingdom 1488alive104.16
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable5.70
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive116.49
Binding MOAD - Binding Mother of All Databases
United States 148alive12.21
CancerPPD
India 0alive0.00
Cancer3D United States 10alive4.95
PLAZA - An online platform for plant comparative genomics Belgium 196unstable21.56
NDB - Nucleic Acid Database
United States 28alive9.15
RNA Bricks
Poland 20alive6.60
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive13.00
UniCarbKB - UniCarb KnowledgeBase Australia 85alive14.03
Pfam - Protein Families Database United Kingdom 19906alive995.30
Gene3D - Gene3D United Kingdom 194alive21.56
LenVarDB - Database of length variant protein domains
India 2alive0.67
FireDB - Database of Annotated Functionally Important Residues
Spain 59alive5.90
SCOP2 - Structural Classification of Proteins 2
United Kingdom 50alive16.50
ArchDB
Spain 84alive6.46
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
3did - 3-Dimensional Interacting Domains
Spain 399unstable29.59
Negatome - The Negatome Database
Germany 109unstable14.79
GPCRDB - G Protein-coupled Receptor (GPCR) Database Denmark 964alive50.23
CSA - Catalytic Site Atlas
United Kingdom 614unstable42.04
CAZy - Carbohydrate-active Enzymes Database
France 553alive184.33
ASD - Allosteric Database
China 94alive15.67
SFLD - Structure Function Linkage Database
United States 231alive20.79
canSAR United Kingdom 70unstable13.30
ChEMBL
United Kingdom 1746unstable300.31
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22alive7.33
SAbDab - The Structural Antibody Database United Kingdom 23unstable6.59
AVPdb
India 16alive5.33
CAMP - Collection of Anti-Microbial Peptides
India 218alive30.52
MetalPDB - Meta knowledge on Protein Data Bank
Italy 18alive4.50
eProS - Energy Profile Suite
Germany 4unstable0.37
GFDB - Glycan Fragment Database
United States 10alive2.50
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive12.50
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.55
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive37.85
PaVE - PapillomaVirus Episteme United States 83unstable8.09
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive5.94
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive45.40
RhesusBase China 12unstable2.79
ConoServer - Database for Conopeptides Australia 205unstable19.13
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 209unstable3.40
Polbase - Polymerase Database United States 8unstable0.43
BitterDB
Israel 57alive11.40
COD - Crystallography Open Database
Lithuania 263alive32.55
RNA CoSSMos - RNA Characterization of Secondary Structure Motifs Database
United States 18alive3.60
MMDB - Macromolecular Database
United States 79unstable7.74
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
IndelFR - Indel Flanking Region Database
China 12dead0.00
NRG-CING - NMR Restraints Grid -Common Interface for NMR structure Generation
Netherlands 29unstable1.16
STAP
Korea Rep. 11alive2.18
PASS2 - Protein Alignments organised as Structural Superfamilies India 70alive4.67
PSCDB - Protein Structural Change DataBase Japan 35alive5.83
SNPeffect - Single Nucleotide Variants Belgium 261alive21.75
AREsite - AU-rich Elements Site Austria 110alive18.15
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable3.12
BriX
Belgium 78alive11.14
BSDB - Bio-molecule Stretching Database
Poland 21alive3.47
CDDB - Conformational Dynamics Databank
United States 11unstable1.01
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 8unstable0.88
TOPSAN - The Open Protein Structure Annotation Network
United States 63unstable5.67
ODB - Operon DataBase Japan 79alive9.88
BISC - BInary SubComplex Database
United Kingdom 3unstable0.19
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.67
ProtCID - Protein Common Interfaces Database United States 44alive7.26
DAnCER - Disease Annotated Chromatin Epigenetics Resource Canada 17alive2.78
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.86
PDBWiki Germany 24alive3.43
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.33
wwpdb - worldwide protein data bank archive
United States 8alive1.98
PMP - Protein Model Portal Switzerland 43unstable10.21
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.56
CREDO
United Kingdom 11alive2.64
PolyprOnline France 2unstable0.63
PTM-SD - Post Translational Modification Structural Database France 6alive2.00
Kin-Driver Argentina 7unstable2.17
BCL2DB - BCL-2 Database
France 4unstable0.41
CHOPIN United Kingdom 1alive0.50
3DGD - 3D Genome Database China 6unstable1.08
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
3D-interologs - 3D-domain interactions based on homologous proteins
Taiwan 18alive2.57
KNApSAcK-3D - KNApSAcK-3D Japan 11alive2.75
SKEMPI - Structual database of Kinetics and Energetics of Mutant Protein Interactions
Spain 53alive10.60
Plant-PrAS - Plant-Protein Annotation Suite Japan 4alive2.00
PolysacDB India 4alive0.80
SKPDB - ShiKimate Pathway DataBase Brazil 22dead0.00
RNA FRABASE 2.0 - RNA FRAgments search engine & dataBASE
Poland 60alive8.23
MUFOLD-DB - A Solution For Protein 3D Structure Prediction
United States 1alive0.33
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.72
CoDNaS - Conformational Diversity of Native State
Argentina 19unstable1.95
GPCR-RD - A Database For Experimental Restaints Of GPCRs United States 38alive5.43
CyanoPhyChe India 2alive0.40
eBLOCKs - eBLOCKs
United States 28dead0.00
PDBSITE Russian Federation 92alive7.59
ADDA
Finland 44dead0.00
FunShift
Sweden 44alive3.67
ProDom France 251alive20.92
S4
United Kingdom 20dead0.00
SBASE
Italy 23unstable1.21
SYSTERS
Germany 51unstable2.51
PDB-Ligand Korea Rep. 58unstable1.84
CSS - Carbohydrate Structure Suite
Germany 121dead0.00
GenDiS - Genomic Distribution of Protein Structural Domain Superfamilies India 16alive1.33
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343unstable25.44
STING Report
Brazil 22alive1.83
PFD - Protein Folding Database Australia 30unstable1.45
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive32.69
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive4.25
3D-footprint
Spain 34alive4.86
MeMotif - A wiki for motifs in transmembrane proteins
Germany 15alive2.14
3DNALandscapes
United States 11unstable0.91
NNDB - Nearest Neighbor Database
United States 138alive19.71
ComSin
Russian Federation 22alive3.05
fPOP - footprinting Pockets Of Proteins
United States 11dead0.00
PGD - Protein Geometry Database United States 19unstable2.14
PTGL - Protein Topology Graph Library Germany 10dead0.00
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive3.17
RAD - Rice Annotation Database Japan 15unstable0.39
DBD - Transcription factor prediction database United Kingdom 156unstable12.91
MeRNA - A Database of Metal Ion Binding Sites in RNA Structures
United States 49dead0.00
CyBase
Australia 220unstable9.00
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.73
ProTherm - Thermodynamic Database for Proteins and Mutants Japan 618dead0.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable10.79
REFOLD
Australia 81dead0.00
DiProDB - Dinucleotide Property Database
United Kingdom 31alive3.72
BPS
United States 32unstable2.32
SitesBase
United Kingdom 91dead0.00
BIOZON
United States 53unstable4.29
NRED - Noncoding RNA Expression Database Australia 152alive19.00
MulPSSM - A Database of Multiple Position-specific Scoring Matrices of Protein Domain Families
India 28unstable0.59
PseudoBase++ - An extension of PseudoBase United States 38alive4.75
SuperSite
Germany 28unstable3.19
DMAPS - Database of Multiple Alignments for Protein Structures
United States 10dead0.00
FSN - Flexible Structural Neighborhood
United States 13alive1.18
MolMovDB - Database of Macromolecular Movements
United States 652unstable30.20
PMDB - Protein Model Database Italy 194unstable2.82
MMsINC - Molecular Modeling Section
Italy 55alive6.88
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable186.66
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.97
CC+
United Kingdom 78alive9.75
ConSurf-DB
Israel 104alive13.00
Circular Permutation Database
Taiwan 36alive4.45
GTOP - Genomes TO Protein Structures and Functions database Japan 26alive3.15
JAIL - Just another interface library
Germany 7alive0.88
KineticDB
Russian Federation 53unstable5.03
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive9.38
SPROUTS - Structural Prediction for pRotein fOlding UTility System
United States 21dead0.00
Voronoia - Voronoia Germany 52alive6.50
VIPERdb - Virus Particle Explorer United States 293alive26.64
Bionemo - Biodegradation Network Molecular Biology Database
Spain 15alive1.88
ExDom - ExDom United States 10unstable0.36
BodyParts3D Japan 30dead0.00
MoKCa - Mutations, Oncogenes, Knowledge & Cancer United Kingdom 34alive4.21
APD - Antimicrobial Peptide Database United States 572alive70.07
ProSAS - Protein Structure and Alternative Splicing database Germany 24unstable1.17
BMRB - Biological Magnetic Resonance Data Bank
United States 635alive70.56
BioHealthBase United States 70unstable6.77
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive7.59
MALISAM - Manual Alignments For Structurally Analogous Motifs
United States 20alive2.20
MegaMotifbase - Structural Motifs in Protein Families and Superfamilies
India 24alive2.67
HPD - heme protein structure–electrochemical function database
United States 68dead0.00
GDB:Structures - Glycoconjugate Data Bank:Structures
Japan 33alive3.67
RNAJunction - RNAJunction
United States 106dead0.00
MAPU - Max-Planck Unified proteome database Germany 53alive5.30
PROTCOM - Protein Complexes United States 53dead0.00
SNAPPI-DB - SNAPPI-DB
United Kingdom 60alive6.00
BindingDB - BindingDB
United States 706alive69.89
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.76
Defensins knowledgebase - Defensins knowledgebase
Singapore 81alive8.10
GlycoMapsDB - GlycoMapsDB Germany 46alive4.60
T-DB - TOPOFIT-DB
United States 19dead0.00
euHCVdb - European HCV Database United States 118unstable3.66
SGCEdb United States 2dead0.00
LMPD - LIPID MAPS Proteome Database
United States 43alive3.91
AffinDB - Affinity database for protein-ligand complexes
Germany 84alive7.64
SuperNatural
Germany 56alive5.09
Epitome - Epitome
United States 58unstable3.80
DisProt - Database of Protein Disorder United States 838alive69.14
RBP-Var China 0alive0.00
PDBFlex United States 1alive1.00
EK3D - E.coli Kantigen 3D structure Database India 0alive0.00
SIB - Swiss Institute of Bioinformatics
Switzerland 6unstable1.80
BIGNASim - BIGNASim database structure and analysis portal for nucleic acids simulation data
Spain 1alive1.00
UET - Universal Evolutionary Trace United States 1alive0.98
EBI - The European Bioinformatics Institute United Kingdom 610unstable23.87
iGNM - Gaussian Network Model Database United States 116alive9.67
EMDataBank - Unified Data Resource for 3-Dimensional Electron Microscopy
United States 1alive0.99
DBAASP - Database of Antimicrobial Activity and Structure of Peptides Georgia 9alive3.00
Start2Fold Belgium 1alive1.00
InterRNA - INTERactions in RNA structures database
Malaysia 0alive0.00
ONRLDB - Orphan Nuclear Receptor Ligand Binding Database
India 0alive0.00
SATPdb - A database of structurally annotated therapeutic peptides
India 1alive1.00
Ebola-KB - Ebola virus-centered Knowledge Base United States 0alive0.00
DMDD - Deciphering the Mechanisms of Developmental Disorders United Kingdom 13unstable1.01
CSDB - Carbohydrate Structure Database
Russian Federation 0alive0.00
NBDB - Nucleotide binding database
Singapore 1alive0.99
BDB - Biopanning Data Bank
China 0unstable0.00
OpenTein - Open Teratoma Investigation Japan 0alive0.00
KLIFS Netherlands 2alive1.98
PDBe - Protein Data Bank in Europe United Kingdom 239alive34.14
GlyTouCan - A Glycan Repository
Japan 3unstable2.76
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.97
PubChem 
United States 1412unstable44.13
CSDBs - Carbohydrate Structure Databases Russian Federation 2alive2.00
LNCediting United States 0unstable0.00
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive2.00
LinkProt Poland 0alive0.00
Membranome - Membrane Proteome United States 1unstable0.65
PDBj - Protein Data Bank Japan Japan 94unstable1.61
ECOD - Evolutionary Classification of Protein Domains United States 33alive11.00
TSTMP - Target Selection for human TransMembrane Proteins
Hungary 0alive0.00
IRD - Influenza Research Database United States 165dead0.00
URSDB - Universe of RNA Structures DataBase
Russian Federation 0alive0.00
3DFlu Poland 0alive0.00
TMPL - Transmembrane protein Models Positioned in the Lipid bilayer
France 0alive0.00
TOPDOM - database of conservatively located domains and motifs in proteins
Hungary 27alive3.00
Cyclo-lib - a database of computational molecular dynamics simulations of cyclodextrins
Spain 0alive0.00
FoldAtlas United Kingdom 1alive1.00
Pro54DB - σ54 promoter database China 0unstable0.00
* Citations derived from Google Scholar.
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