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 8alive2.67
CDD - Conserved Domain Database
United States 4407unstable181.18
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 8unstable2.45
RCSB PDB - RCSB Protein Data Bank United States 853unstable73.11
CATH
United Kingdom 1488alive98.21
Genome3D - Annotating Genomes with Structures United Kingdom 42alive5.04
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive99.85
Binding MOAD - Binding Mother of All Databases
United States 148alive11.27
CancerPPD
India 0alive0.00
Cancer3D United States 10alive3.30
PLAZA - An online platform for plant comparative genomics Belgium 196unstable14.59
NDB - Nucleic Acid Database
United States 28alive6.93
RNA Bricks
Poland 20alive4.95
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive9.56
UniCarbKB - UniCarb KnowledgeBase Australia 85alive11.90
Pfam - Protein Families Database United Kingdom 19906alive947.90
Gene3D - Gene3D United Kingdom 194alive19.40
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
ArchDB
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 399unstable20.56
Negatome - The Negatome Database
Germany 109alive13.08
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 70unstable10.85
ChEMBL
United Kingdom 1746unstable189.15
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22alive5.45
SAbDab - The Structural Antibody Database United Kingdom 23unstable4.83
AVPdb
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 4unstable0.22
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 83unstable4.98
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 23alive3.76
OPM - Orientations of Proteins in Membranes Database
United States 142alive22.96
NucleaRDB - Information System for Nuclear Receptors
Netherlands 209unstable2.46
Polbase - Polymerase Database United States 8unstable0.28
BitterDB
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 79unstable4.87
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 3alive0.49
IndelFR - Indel Flanking Region Database
China 12unstable0.24
NRG-CING - NMR Restraints Grid -Common Interface for NMR structure Generation
Netherlands 29unstable0.73
STAP
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 26unstable2.90
BriX
Belgium 78alive9.56
BSDB - Bio-molecule Stretching Database
Poland 21alive2.97
CDDB - Conformational Dynamics Databank
United States 11unstable1.04
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 8unstable0.57
TOPSAN - The Open Protein Structure Annotation Network
United States 63unstable3.86
ODB - Operon DataBase Japan 79unstable7.29
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 17unstable2.23
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 14alive2.00
wwpdb - worldwide protein data bank archive
United States 8alive1.58
PMP - Protein Model Portal Switzerland 43unstable6.19
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable0.94
CREDO
United Kingdom 11unstable1.78
PolyprOnline France 2unstable0.42
PTM-SD - Post Translational Modification Structural Database France 6alive1.49
Kin-Driver Argentina 7unstable1.66
BCL2DB - BCL-2 Database
France 4unstable0.48
CHOPIN United Kingdom 1unstable0.32
3DGD - 3D Genome Database China 6unstable0.72
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 8unstable0.74
CoDNaS - Conformational Diversity of Native State
Argentina 19unstable2.09
GPCR-RD - A Database For Experimental Restaints Of GPCRs United States 38alive4.75
CyanoPhyChe India 2alive0.33
eBLOCKs - eBLOCKs
United States 28dead0.00
PDBSITE Russian Federation 92alive7.01
ADDA
Finland 44dead0.00
FunShift
Sweden 44unstable2.78
ProDom France 251alive19.31
S4
United Kingdom 20dead0.00
SBASE
Italy 23unstable0.83
SYSTERS
Germany 51unstable2.71
PDB-Ligand Korea Rep. 58unstable1.83
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 30unstable1.02
PEDANT - Protein Extraction, Description and ANalysis Tool Germany 523alive30.46
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive3.88
3D-footprint
Spain 34alive4.25
MeMotif - A wiki for motifs in transmembrane proteins
Germany 15alive1.88
3DNALandscapes
United States 11unstable0.61
NNDB - Nearest Neighbor Database
United States 138alive17.25
ComSin
Russian Federation 22alive2.67
fPOP - footprinting Pockets Of Proteins
United States 11dead0.00
PGD - Protein Geometry Database United States 19unstable1.43
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 156unstable12.09
MeRNA - A Database of Metal Ion Binding Sites in RNA Structures
United States 49dead0.00
CyBase
Australia 220unstable10.63
PINT - Protein–protein Interactions Thermodynamic Database Japan 57unstable3.37
ProTherm - Thermodynamic Database for Proteins and Mutants Japan 618dead0.00
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions Japan 283unstable11.49
REFOLD
Australia 81dead0.00
DiProDB - Dinucleotide Property Database
United Kingdom 31unstable3.03
BPS
United States 32unstable1.56
SitesBase
United Kingdom 91dead0.00
BIOZON
United States 53unstable4.02
NRED - Noncoding RNA Expression Database Australia 152alive16.89
MulPSSM - A Database of Multiple Position-specific Scoring Matrices of Protein Domain Families
India 28unstable0.42
PseudoBase++ - An extension of PseudoBase United States 38alive4.10
SuperSite
Germany 28unstable2.18
DMAPS - Database of Multiple Alignments for Protein Structures
United States 10dead0.00
FSN - Flexible Structural Neighborhood
United States 13alive1.07
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 7583unstable129.99
AS-ALPS - Alternative Splicing-induced Alteration of Protein Structure Japan 25unstable2.64
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 26unstable2.74
JAIL - Just another interface library
Germany 7alive0.78
KineticDB
Russian Federation 53unstable3.42
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 10unstable0.24
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 24unstable0.79
BMRB - Biological Magnetic Resonance Data Bank
United States 635alive63.50
BioHealthBase United States 70unstable5.11
3D RIBOSOMAL MODIFICATION MAPS DATABASE United States 69alive6.83
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 33unstable2.90
RNAJunction - RNAJunction
United States 106dead0.00
MAPU - Max-Planck Unified proteome database Germany 53unstable4.43
PROTCOM - Protein Complexes United States 53dead0.00
SNAPPI-DB - SNAPPI-DB
United Kingdom 60alive5.45
BindingDB - BindingDB
United States 706alive61.61
PIDD - Protein Inter-Atomic Distance Distribution Database United States 10unstable0.53
Defensins knowledgebase - Defensins knowledgebase
Singapore 81alive7.22
GlycoMapsDB - GlycoMapsDB Germany 46alive4.18
T-DB - TOPOFIT-DB
United States 19dead0.00
euHCVdb - European HCV Database United States 118unstable5.15
SGCEdb United States 2dead0.00
LMPD - LIPID MAPS Proteome Database
United States 43alive3.58
AffinDB - Affinity database for protein-ligand complexes
Germany 84alive7.00
SuperNatural
Germany 56alive4.67
Epitome - Epitome
United States 58unstable3.82
DisProt - Database of Protein Disorder United States 838alive63.82
RBP-Var China 0alive0.00
PDBFlex United States 1alive0.50
EK3D - E.coli Kantigen 3D structure Database India 0alive0.00
SIB - Swiss Institute of Bioinformatics
Switzerland 6unstable1.02
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 610unstable17.28
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 13unstable0.62
CSDB - Carbohydrate Structure Database
Russian Federation 0alive0.00
NBDB - Nucleotide binding database
Singapore 1alive0.48
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 3unstable1.03
CAMPR3 - Collection of Anti-Microbial Peptides India 1alive0.49
PubChem 
United States 1412unstable29.81
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 1unstable0.68
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 0unstable0.00
FoldAtlas United Kingdom 1alive0.99
Pro54DB - σ54 promoter database China 0unstable0.00
* Citations derived from Google Scholar.
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