Construction and analysis of protein–protein interaction networks

Table 1 Databases and resources useful for researching PPIs.

Database	URL	Resources	Refs.
BIND	Peer-reviewed bio-molecular interaction database containing published interactions and complexes	http://bind.ca/	[79]
BioGRID	Protein and genetic interactions from major model organism species	http://www.thebiogrid.org/	[80]
COGs	Orthology data and phylogenetic profiles	http://www.ncbi.nlm.nih.gov/COG/	[81, 82]
DIP	Experimentally determined interactions between proteins	http://dip.doe-mbi.ucla.edu/	[51]
HPRD	Human protein functions, PPIs, post-translational modifications, enzyme–substrate relationships and disease associations	http://www.hprd.org/	[50, 83]
IntAct	Interaction data abstracted from literature or from direct data depositions by expert curators	http://www.ebi.ac.uk/intact/	[84]
iPFAM	Physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB)	http://ipfam.sanger.ac.uk/	[85]
MINT	Experimentally verified PPI mined from the scientific literature by expert curators	http://mint.bio.uniroma2.it/mint/	[86]
Predictome	Experimentally derived and computationally predicted functional linkages	http://visant.bu.edu/	[52]
ProLinks	Protein functional linkages	http://mysql5.mbi.ucla.edu/cgi-bin/functionator/pronav	[87]
SCOPPI	Domain–domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions	http://www.scoppi.org/	[88]
STRING	Protein functional linkages from experimental data and computational predicttions	http://string.embl.de/	[36, 48]