Table 1
Open in new tab

Related databases for PPI prediction

DatabasesDescriptionURLLast UpdateReferences
PPI networksBINDPPIs collected from the species of humans, fruit flies, yeast, nematodes, etc.http://download.baderlab.org/BINDTranslation/2005[4]
DIPExperimentally curated PPI database including biological information of proteins, PPIs and experimental techniques for detecting interactionshttp://dip.doe-mbi.ucla.edu/dip/Main.cgi2020[97]
MINTExperimentally curated PPI database that covers about 117001 PPIs from 607 different specieshttps://mint.bio.uniroma2.it/2012[59]
BiogridComposed of proteins, and their genetic and chemical interactions, currently has more than 1.5 million interactions obtained from high-throughput experimentshttp://www.thebiogrid.org2020[16]
HPRDThe largest human PPI database including protein annotation, PPIs, post-transcriptional modification, subcellular location and other informationhttp://www.hprd.org2010[51]
IntActApproximately 275000 curated binary interaction evidences from more than 5000 publicationshttp://www.ebi.ac.uk/intact2014[70]
STRINGFunctional associations between protein pairs and covers 2031 species, 9643763 proteins and a total of 1380838440 PPIshttps://string-db.org/STRING2019[87]
Protein sequencesUniProtA collection of protein sequences and their annotations with three major components including UniProtKB, UniParc and UniRefhttp://www.uniprot.org2020[20]
PIRProtein sequences and high-quality annotations by integrating more than 90 biological databaseshttp://pir.georgetown.edu2020[7]
SWISS-PROTA database composed of protein sequences and detailed annotations and it has been merged into the UniProt and maintained by EBI nowhttp://www.expasy.ch/sport2020[13]
NRL3DPrimary structures of proteins with known three-dimensional structureshttp://www.ncifcrf.gov/NRL-3D2020[29]
TrEMBLComputer-annotated protein sequences complementary to SWISS-PORThttp://www.expasy.ch/2020[13]
Higher-level structuresPDBExperimentally determined 3D structures of proteins , nucleic acids and sugarhttp://www.rcsb.org/2020[96]
SCOPProteins and their classifications with known structures, and also describes the functions and evolutionary relationships between them in detailshttp://scop.mrc-lmb.cam.ac.uk/scop2020[2]
Genomic informationMIPSHomology data of mammalian proteins, mainly including human, rat, mouse and other specieshttp://mips.gsf.de/proj/ppi/2005[71]
CGDPhylogeny and gene similarity information for proteins.http://www.candidagenome.org/2014[9]
Gene ontologyGO DatabaseThe world’s largest source of information on the functions of genes ranging from the molecular to the organism levelhttp://www.geneontology.org2020[19]
QuickGOA fast web-based browser of the GO and GO annotation datahttp://www.ebi.ac.uk/QuickGO2020[10]
DatabasesDescriptionURLLast UpdateReferences
PPI networksBINDPPIs collected from the species of humans, fruit flies, yeast, nematodes, etc.http://download.baderlab.org/BINDTranslation/2005[4]
DIPExperimentally curated PPI database including biological information of proteins, PPIs and experimental techniques for detecting interactionshttp://dip.doe-mbi.ucla.edu/dip/Main.cgi2020[97]
MINTExperimentally curated PPI database that covers about 117001 PPIs from 607 different specieshttps://mint.bio.uniroma2.it/2012[59]
BiogridComposed of proteins, and their genetic and chemical interactions, currently has more than 1.5 million interactions obtained from high-throughput experimentshttp://www.thebiogrid.org2020[16]
HPRDThe largest human PPI database including protein annotation, PPIs, post-transcriptional modification, subcellular location and other informationhttp://www.hprd.org2010[51]
IntActApproximately 275000 curated binary interaction evidences from more than 5000 publicationshttp://www.ebi.ac.uk/intact2014[70]
STRINGFunctional associations between protein pairs and covers 2031 species, 9643763 proteins and a total of 1380838440 PPIshttps://string-db.org/STRING2019[87]
Protein sequencesUniProtA collection of protein sequences and their annotations with three major components including UniProtKB, UniParc and UniRefhttp://www.uniprot.org2020[20]
PIRProtein sequences and high-quality annotations by integrating more than 90 biological databaseshttp://pir.georgetown.edu2020[7]
SWISS-PROTA database composed of protein sequences and detailed annotations and it has been merged into the UniProt and maintained by EBI nowhttp://www.expasy.ch/sport2020[13]
NRL3DPrimary structures of proteins with known three-dimensional structureshttp://www.ncifcrf.gov/NRL-3D2020[29]
TrEMBLComputer-annotated protein sequences complementary to SWISS-PORThttp://www.expasy.ch/2020[13]
Higher-level structuresPDBExperimentally determined 3D structures of proteins , nucleic acids and sugarhttp://www.rcsb.org/2020[96]
SCOPProteins and their classifications with known structures, and also describes the functions and evolutionary relationships between them in detailshttp://scop.mrc-lmb.cam.ac.uk/scop2020[2]
Genomic informationMIPSHomology data of mammalian proteins, mainly including human, rat, mouse and other specieshttp://mips.gsf.de/proj/ppi/2005[71]
CGDPhylogeny and gene similarity information for proteins.http://www.candidagenome.org/2014[9]
Gene ontologyGO DatabaseThe world’s largest source of information on the functions of genes ranging from the molecular to the organism levelhttp://www.geneontology.org2020[19]
QuickGOA fast web-based browser of the GO and GO annotation datahttp://www.ebi.ac.uk/QuickGO2020[10]
Table 1
Open in new tab

Related databases for PPI prediction

DatabasesDescriptionURLLast UpdateReferences
PPI networksBINDPPIs collected from the species of humans, fruit flies, yeast, nematodes, etc.http://download.baderlab.org/BINDTranslation/2005[4]
DIPExperimentally curated PPI database including biological information of proteins, PPIs and experimental techniques for detecting interactionshttp://dip.doe-mbi.ucla.edu/dip/Main.cgi2020[97]
MINTExperimentally curated PPI database that covers about 117001 PPIs from 607 different specieshttps://mint.bio.uniroma2.it/2012[59]
BiogridComposed of proteins, and their genetic and chemical interactions, currently has more than 1.5 million interactions obtained from high-throughput experimentshttp://www.thebiogrid.org2020[16]
HPRDThe largest human PPI database including protein annotation, PPIs, post-transcriptional modification, subcellular location and other informationhttp://www.hprd.org2010[51]
IntActApproximately 275000 curated binary interaction evidences from more than 5000 publicationshttp://www.ebi.ac.uk/intact2014[70]
STRINGFunctional associations between protein pairs and covers 2031 species, 9643763 proteins and a total of 1380838440 PPIshttps://string-db.org/STRING2019[87]
Protein sequencesUniProtA collection of protein sequences and their annotations with three major components including UniProtKB, UniParc and UniRefhttp://www.uniprot.org2020[20]
PIRProtein sequences and high-quality annotations by integrating more than 90 biological databaseshttp://pir.georgetown.edu2020[7]
SWISS-PROTA database composed of protein sequences and detailed annotations and it has been merged into the UniProt and maintained by EBI nowhttp://www.expasy.ch/sport2020[13]
NRL3DPrimary structures of proteins with known three-dimensional structureshttp://www.ncifcrf.gov/NRL-3D2020[29]
TrEMBLComputer-annotated protein sequences complementary to SWISS-PORThttp://www.expasy.ch/2020[13]
Higher-level structuresPDBExperimentally determined 3D structures of proteins , nucleic acids and sugarhttp://www.rcsb.org/2020[96]
SCOPProteins and their classifications with known structures, and also describes the functions and evolutionary relationships between them in detailshttp://scop.mrc-lmb.cam.ac.uk/scop2020[2]
Genomic informationMIPSHomology data of mammalian proteins, mainly including human, rat, mouse and other specieshttp://mips.gsf.de/proj/ppi/2005[71]
CGDPhylogeny and gene similarity information for proteins.http://www.candidagenome.org/2014[9]
Gene ontologyGO DatabaseThe world’s largest source of information on the functions of genes ranging from the molecular to the organism levelhttp://www.geneontology.org2020[19]
QuickGOA fast web-based browser of the GO and GO annotation datahttp://www.ebi.ac.uk/QuickGO2020[10]
DatabasesDescriptionURLLast UpdateReferences
PPI networksBINDPPIs collected from the species of humans, fruit flies, yeast, nematodes, etc.http://download.baderlab.org/BINDTranslation/2005[4]
DIPExperimentally curated PPI database including biological information of proteins, PPIs and experimental techniques for detecting interactionshttp://dip.doe-mbi.ucla.edu/dip/Main.cgi2020[97]
MINTExperimentally curated PPI database that covers about 117001 PPIs from 607 different specieshttps://mint.bio.uniroma2.it/2012[59]
BiogridComposed of proteins, and their genetic and chemical interactions, currently has more than 1.5 million interactions obtained from high-throughput experimentshttp://www.thebiogrid.org2020[16]
HPRDThe largest human PPI database including protein annotation, PPIs, post-transcriptional modification, subcellular location and other informationhttp://www.hprd.org2010[51]
IntActApproximately 275000 curated binary interaction evidences from more than 5000 publicationshttp://www.ebi.ac.uk/intact2014[70]
STRINGFunctional associations between protein pairs and covers 2031 species, 9643763 proteins and a total of 1380838440 PPIshttps://string-db.org/STRING2019[87]
Protein sequencesUniProtA collection of protein sequences and their annotations with three major components including UniProtKB, UniParc and UniRefhttp://www.uniprot.org2020[20]
PIRProtein sequences and high-quality annotations by integrating more than 90 biological databaseshttp://pir.georgetown.edu2020[7]
SWISS-PROTA database composed of protein sequences and detailed annotations and it has been merged into the UniProt and maintained by EBI nowhttp://www.expasy.ch/sport2020[13]
NRL3DPrimary structures of proteins with known three-dimensional structureshttp://www.ncifcrf.gov/NRL-3D2020[29]
TrEMBLComputer-annotated protein sequences complementary to SWISS-PORThttp://www.expasy.ch/2020[13]
Higher-level structuresPDBExperimentally determined 3D structures of proteins , nucleic acids and sugarhttp://www.rcsb.org/2020[96]
SCOPProteins and their classifications with known structures, and also describes the functions and evolutionary relationships between them in detailshttp://scop.mrc-lmb.cam.ac.uk/scop2020[2]
Genomic informationMIPSHomology data of mammalian proteins, mainly including human, rat, mouse and other specieshttp://mips.gsf.de/proj/ppi/2005[71]
CGDPhylogeny and gene similarity information for proteins.http://www.candidagenome.org/2014[9]
Gene ontologyGO DatabaseThe world’s largest source of information on the functions of genes ranging from the molecular to the organism levelhttp://www.geneontology.org2020[19]
QuickGOA fast web-based browser of the GO and GO annotation datahttp://www.ebi.ac.uk/QuickGO2020[10]
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