A Survey on Identification of Protein Complexes in Protein–protein Interaction Data: Methods and Evaluation - Computational Intelligence Techniques for Comparative Genomics - page 65

Table 1 Protein interaction databases
S. No Database
name

Total no. of
interactions

References Source link Number of

species/
organisms

1 BioGrid 7,17,604 Stark et al. [ 36 ] http://thebiogrid.org/ 60

2 DIP 76,570 Xenarios et al.

[ 37 ]

http://dip.doe-mbi.ucla.edu/
dip/Main.cgi/

637

3 Hit

predict

2,39,584 Patil et al. [ 38 ] http://hintdb.hgc.jp/htp/ 9

4 MINT 2,41,458 Chatr-aryamontri

et al. [ 39 ]

http://mint.bio.uniroma2.it/
mint/

30

5 IntAct 4,33,135 Hermjakob et al.

[ 40 ]

http://www.ebi.ac.uk/intact/ 8

6 APID 3,22,579 Prirto and de Las

Rivas [ 41 ]

http://bioinfow.dep.usal.es/
apid/index.html/

15

7 BIND 3,00,000+ Bader et al. [ 42 ] http://bind.ca/

-

8 PINA

2.0

3,00,155 Cowley et al. [ 43 ] http://cbg.garvan.unsw.edu.

au/pina/

7

an elaborate description of the manner in which the PPI data were derived exper-
imentally, often including links directly to the concluding evidence from the lit-
erature [ 24 ]. The database of interacting proteins (DIP) is another database of
experimentally determined protein protein binary interactions [ 25 ]. The biological

general repository for interaction datasets (BioGRID) is a database that contains
protein and genetic interactions among thirteen different species [ 26 ]. Interactions
are regularly added through exhaustive curation of the primary literature to the
databases. Interaction data are extracted from other databases including BIND and
Munich Information Center for protein sequences (MIPS) [ 27 ], as well as directly
from large-scale experiments [ 28 ]. Hit predict is a resource of high con

-

dence PPIs
from which we can get the total number of interactions in a species for a protein and
can view all the interactions with con dence scores [ 29 ].

The Molecular INTeraction (MINT) database is another database of experi-
mentally derived PPI data extracted from the literature, with the added element of
providing the weight of evidence for each interaction [ 25 ]. The Human Protein
Interaction Database (HPID) was designed to provide human protein interaction
information precomputed from existing structural and experimental data [ 30 ]. The
Information Hyperlinked over Proteins (iHOP) database can be searched to identify
previously reported interactions in PubMed for a protein of interest [ 31 ]. IntAct [ 32 ]
provides an open source database and toolkit for the storage, presentation, and
analysis of protein interactions [ 33 ].
The web interface provides both textual and graphical representations of protein
interactions and allows exploring interaction networks in the context of the GO
annotations of the interacting proteins [ 24 ]. However, we have observed that the