Database Commons a catalog of biological databases

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Data type:

Database name Data type(s) Major organism(s) Location Citation* Status z-index
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive2.67
CDD - Conserved Domain Database
United States 4407unstable171.38
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive56.84
KnotProt - A database of proteins with knots and slipknots
Poland 67alive11.17
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable2.40
RCSB PDB - RCSB Protein Data Bank United States 853unstable69.46
United Kingdom 1488alive98.21
Genome3D - Annotating Genomes with Structures United Kingdom 42alive5.04
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive97.83
Binding MOAD - Binding Mother of All Databases
United States 148alive11.27
India 0alive0.00
Cancer3D United States 10unstable3.17
PLAZA - An online platform for plant comparative genomics Belgium 196unstable13.72
NDB - Nucleic Acid Database
United States 28alive6.93
RNA Bricks
Poland 20alive4.95
TFBSshape - DNA shape features of transcription factor binding sites United States 39unstable8.97
UniCarbKB - UniCarb KnowledgeBase Australia 85alive11.90
Pfam - Protein Families Database United Kingdom 19906alive947.90
Gene3D - Gene3D United Kingdom 194alive19.21
LenVarDB - Database of length variant protein domains
India 2alive0.50
FireDB - Database of Annotated Functionally Important Residues
Spain 59alive5.36
SCOP2 - Structural Classification of Proteins 2
United Kingdom 50alive12.38
Spain 84alive6.00
pE-DB - Protein Ensemble Database Belgium 55unstable12.93
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
3did - 3-Dimensional Interacting Domains
Spain 399unstable19.64
Negatome - The Negatome Database
Germany 109unstable12.94
GPCRDB - G Protein-coupled Receptor (GPCR) Database Denmark 964alive47.72
CSA - Catalytic Site Atlas
United Kingdom 614unstable38.59
CAZy - Carbohydrate-active Enzymes Database
France 553alive138.25
ASD - Allosteric Database
China 94alive13.43
SFLD - Structure Function Linkage Database
United States 231alive19.06
canSAR United Kingdom 70unstable10.27
United Kingdom 1746unstable180.42
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22unstable5.17
SAbDab - The Structural Antibody Database United Kingdom 23unstable4.54
India 16alive4.00
CAMP - Collection of Anti-Microbial Peptides
India 218alive26.98
MetalPDB - Meta knowledge on Protein Data Bank
Italy 18alive3.60
eProS - Energy Profile Suite
Germany 4unstable0.21
GFDB - Glycan Fragment Database
United States 10alive2.00
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive10.00
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.14
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive35.14
PaVE - PapillomaVirus Episteme United States 83unstable4.65
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive4.75
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive39.72
RhesusBase China 12unstable2.26
ConoServer - Database for Conopeptides Australia 205unstable18.04
MIPModDB - Major Intrinsic Protein Database
India 23alive3.72
OPM - Orientations of Proteins in Membranes Database
United States 142unstable21.54
NucleaRDB - Information System for Nuclear Receptors
Netherlands 209unstable2.34
Polbase - Polymerase Database United States 8unstable0.25
Israel 57alive9.50
COD - Crystallography Open Database
Lithuania 263alive28.93
RNA CoSSMos - RNA Characterization of Secondary Structure Motifs Database
United States 18alive3.00
MMDB - Macromolecular Database
United States 79unstable4.61
AH-DB - Apo and Holo Structures DataBase
Taiwan 9alive1.50
United Kingdom 7alive1.17
ccPDB - Compilation and Creation of datasets from PDB
India 12alive2.00
Cube-DB - Cube-DB Singapore 3alive0.49
IndelFR - Indel Flanking Region Database
China 12unstable0.24
NRG-CING - NMR Restraints Grid -Common Interface for NMR structure Generation
Netherlands 29unstable0.68
Korea Rep. 11alive1.82
PASS2 - Protein Alignments organised as Structural Superfamilies India 70alive4.38
PSCDB - Protein Structural Change DataBase Japan 35alive5.00
SNPeffect - Single Nucleotide Variants Belgium 261alive20.08
AREsite - AU-rich Elements Site Austria 110alive15.56
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable2.97
Belgium 78alive9.56
BSDB - Bio-molecule Stretching Database
Poland 21alive2.97
CDDB - Conformational Dynamics Databank
United States 11unstable1.07
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 8unstable0.54
TOPSAN - The Open Protein Structure Annotation Network
United States 63unstable4.02
ODB - Operon DataBase Japan 79unstable6.93
BISC - BInary SubComplex Database
United Kingdom 3unstable0.12
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.43
ProtCID - Protein Common Interfaces Database United States 44alive6.22
DAnCER - Disease Annotated Chromatin Epigenetics Resource Canada 17unstable2.26
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.63
PDBWiki Germany 24alive3.00
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive1.98
wwpdb - worldwide protein data bank archive
United States 8alive1.58
PMP - Protein Model Portal Switzerland 43unstable5.85
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable0.90
United Kingdom 11unstable1.80
PolyprOnline France 2unstable0.41
PTM-SD - Post Translational Modification Structural Database France 6alive1.49
Kin-Driver Argentina 7unstable1.66
BCL2DB - BCL-2 Database
France 4unstable0.51
CHOPIN United Kingdom 1unstable0.31
3DGD - 3D Genome Database China 6unstable0.67
PHI-DAC - protein homology database through dihedral angle conservation Israel 0unstable0.00
3D-interologs - 3D-domain interactions based on homologous proteins
Taiwan 18alive2.25
KNApSAcK-3D - KNApSAcK-3D Japan 11alive2.20
SKEMPI - Structual database of Kinetics and Energetics of Mutant Protein Interactions
Spain 53alive8.74
Plant-PrAS - Plant-Protein Annotation Suite Japan 4alive1.33
PolysacDB India 4alive0.67
SKPDB - ShiKimate Pathway DataBase Brazil 22dead0.00
RNA FRABASE 2.0 - RNA FRAgments search engine & dataBASE
Poland 60alive7.28
MUFOLD-DB - A Solution For Protein 3D Structure Prediction
United States 1alive0.24
MPID-T2 - MHC-Peptide Interaction Database-TR version 2 Australia 8unstable0.77
CoDNaS - Conformational Diversity of Native State
Argentina 19unstable2.20
GPCR-RD - A Database For Experimental Restaints Of GPCRs United States 38alive4.75
CyanoPhyChe India 2alive0.33
United States 28dead0.00
PDBSITE Russian Federation 92alive7.01
Finland 44dead0.00
Sweden 44unstable2.64
ProDom France 251alive19.31
United Kingdom 20dead0.00
Italy 23unstable0.80
Germany 51unstable2.79
PDB-Ligand Korea Rep. 58unstable1.96
CSS - Carbohydrate Structure Suite
Germany 121dead0.00
GenDiS - Genomic Distribution of Protein Structural Domain Superfamilies India 16alive1.22
PDBsum - Pictorial database of 3D structures in the Protein Data Bank United Kingdom 343unstable22.95
STING Report
Brazil 22alive1.69
PFD - Protein Folding Database Australia 30unstable0.95
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive29.84
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive3.88
Spain 34alive4.25
MeMotif - A wiki for motifs in transmembrane proteins
Germany 15alive1.88
United States 11unstable0.56
NNDB - Nearest Neighbor Database
United States 138alive17.25
Russian Federation 22alive2.67
fPOP - footprinting Pockets Of Proteins
United States 11dead0.00
PGD - Protein Geometry Database United States 19unstable1.33
PTGL - Protein Topology Graph Library Germany 10dead0.00
Organelle DB - A Database of Organelles and Protein Complexes United States 38alive2.92
RAD - Rice Annotation Database Japan 15unstable0.45
DBD - Transcription factor prediction database United Kingdom 156unstable12.22
MeRNA - A Database of Metal Ion Binding Sites in RNA Structures
United States 49dead0.00
Australia 220unstable11.00
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.47
ProTherm - Thermodynamic Database for Proteins and Mutants Japan 618dead0.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable11.82
Australia 81dead0.00
DiProDB - Dinucleotide Property Database
United Kingdom 31unstable3.03
United States 32unstable1.46
United Kingdom 91dead0.00
United States 53unstable3.80
NRED - Noncoding RNA Expression Database Australia 152alive16.89
MulPSSM - A Database of Multiple Position-specific Scoring Matrices of Protein Domain Families
India 28unstable0.40
PseudoBase++ - An extension of PseudoBase United States 38alive4.10
Germany 28unstable2.05
DMAPS - Database of Multiple Alignments for Protein Structures
United States 10dead0.00
FSN - Flexible Structural Neighborhood
United States 13unstable1.02
MolMovDB - Database of Macromolecular Movements
United States 652unstable29.67
PMDB - Protein Model Database Italy 194unstable1.94
MMsINC - Molecular Modeling Section
Italy 55alive6.11
SWISS-MODEL - The SWISS-MODEL Repository Switzerland 7583unstable124.58
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.64
United Kingdom 78alive8.67
Israel 104alive11.44
Circular Permutation Database
Taiwan 36alive3.96
GTOP - Genomes TO Protein Structures and Functions database Japan 26unstable2.72
JAIL - Just another interface library
Germany 7alive0.78
Russian Federation 53unstable3.24
PSI SGKB - Protein Structure Initiative Structural Genomics Knowledgebase United States 75alive8.33
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
Bionemo - Biodegradation Network Molecular Biology Database
Spain 15alive1.67
ExDom - ExDom United States 10unstable0.23
BodyParts3D Japan 30dead0.00
MoKCa - Mutations, Oncogenes, Knowledge & Cancer United Kingdom 34alive3.74
APD - Antimicrobial Peptide Database United States 572alive62.92
ProSAS - Protein Structure and Alternative Splicing database Germany 24unstable0.74
BMRB - Biological Magnetic Resonance Data Bank
United States 635alive63.50
BioHealthBase United States 70unstable5.04
MALISAM - Manual Alignments For Structurally Analogous Motifs
United States 20alive1.98
MegaMotifbase - Structural Motifs in Protein Families and Superfamilies
India 24alive2.40
HPD - heme protein structure–electrochemical function database
United States 68dead0.00
GDB:Structures - Glycoconjugate Data Bank:Structures
Japan 33unstable2.87
RNAJunction - RNAJunction
United States 106dead0.00
MAPU - Max-Planck Unified proteome database Germany 53unstable4.24
PROTCOM - Protein Complexes United States 53dead0.00
United Kingdom 60alive5.45
BindingDB - BindingDB
United States 706alive61.61
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.50
Defensins knowledgebase - Defensins knowledgebase
Singapore 81alive7.22
GlycoMapsDB - GlycoMapsDB Germany 46alive4.18
United States 19dead0.00
euHCVdb - European HCV Database United States 118unstable5.47
SGCEdb United States 2dead0.00
LMPD - LIPID MAPS Proteome Database
United States 43alive3.58
AffinDB - Affinity database for protein-ligand complexes
Germany 84alive7.00
Germany 56alive4.67
Epitome - Epitome
United States 58unstable3.87
DisProt - Database of Protein Disorder United States 838alive63.82
RBP-Var China 0alive0.00
PDBFlex United States 1unstable0.47
EK3D - E.coli Kantigen 3D structure Database India 0alive0.00
SIB - Swiss Institute of Bioinformatics
Switzerland 6unstable0.96
BIGNASim - BIGNASim database structure and analysis portal for nucleic acids simulation data
Spain 1alive0.50
UET - Universal Evolutionary Trace United States 1alive0.49
EBI - The European Bioinformatics Institute United Kingdom 610unstable16.52
iGNM - Gaussian Network Model Database United States 116alive8.92
EMDataBank - Unified Data Resource for 3-Dimensional Electron Microscopy
United States 1alive0.50
DBAASP - Database of Antimicrobial Activity and Structure of Peptides Georgia 9alive2.25
Start2Fold Belgium 1alive0.50
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 1alive0.50
Ebola-KB - Ebola virus-centered Knowledge Base United States 0unstable0.00
DMDD - Deciphering the Mechanisms of Developmental Disorders United Kingdom 13unstable0.57
CSDB - Carbohydrate Structure Database
Russian Federation 0alive0.00
NBDB - Nucleotide binding database
Singapore 1alive0.49
BDB - Biopanning Data Bank
China 0unstable0.00
OpenTein - Open Teratoma Investigation Japan 0alive0.00
KLIFS Netherlands 2alive0.99
PDBe - Protein Data Bank in Europe United Kingdom 239alive29.88
GlyTouCan - A Glycan Repository
Japan 3unstable0.97
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.49
United States 1412unstable28.24
CSDBs - Carbohydrate Structure Databases Russian Federation 2alive1.00
LNCediting United States 0alive0.00
FuzDB - Database of fuzzy protein complexes Hungary 0alive0.00
JET2 Viewer France 4alive1.33
LinkProt Poland 0unstable0.00
Membranome - Membrane Proteome United States 1unstable0.61
PDBj - Protein Data Bank Japan Japan 94unstable0.70
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
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 27alive2.70
Cyclo-lib - a database of computational molecular dynamics simulations of cyclodextrins
Spain 0alive0.00
FoldAtlas United Kingdom 1alive0.99
Pro54DB - σ54 promoter database China 0unstable0.00
* Citations derived from Google Scholar.