Protein-Protein Interaction Detection: Methods and Analysis

Table 2

The list of web servers with their references.

S. number	Web server	Function	Reference
1	Struct2Net	The Struct2Net server makes structure-based computational predictions of protein-protein interactions (PPIs)	http://groups.csail.mit.edu/cb/struct2net/webserver/
2	Coev2Net	Coev2Net is a general framework to predict, assess, and boost confidence in individual interactions inferred from a high-throughput experiment	http://groups.csail.mit.edu/cb/coev2net/
3	PRISM PROTOCOL	PRISM PROTOCOL is a collection of programs that can be used to predict protein-protein interactions using protein interfaces	http://prism.ccbb.ku.edu.tr/prism_protocol/
4	InterPreTS	InterPreTS uses tertiary structure to predict interactions	http://www.russell.embl.de/interprets
5	PrePPI	PrePPI predicts protein interactions using both structural and nonstructural information	http://bhapp.c2b2.columbia.edu/PrePPI/
6	iWARP	iWARP is a threading-based method to predict protein interaction from protein sequences	http://groups.csail.mit.edu/cb/iwrap/
7	PoiNet	PoiNet provides PPI filtering and network topology from different databases	http://poinet.bioinformatics.tw/
8	PreSPI	PreSPI predicts protein interactions using a combination of domains	http://code.google.com/p/prespi/
9	PIPE2	PIPE2 queries the protein interactions between two proteins based on specificity and sensitivity	http://cgmlab.carleton.ca/PIPE2
10	HomoMINT	HomoMINT predicts interaction in human based on ortholog information in model organisms	http://mint.bio.uniroma2.it/HomoMINT
11	SPPS	SPPS searches protein partners of a source protein in other species	http://mdl.shsmu.edu.cn/SPPS/
12	OrthoMCL-DB	OrthoMCL-DB is a graph-clustering algorithm designed to; identify homologous proteins based on sequence similarity	http://orthomcl.org/orthomcl/
13	P-POD	P-POD provides an easy way to find and visualize the orthologs to a query sequence in the eukaryotes	http://ppod.princeton.edu/
14	COG	COG shows phylogenetic classification of proteins encoded in genomes	http://www.ncbi.nlm.nih.gov/COG/
15	BLASTO	BLASTO performs BLAST based on ortholog group data	http://oxytricha.princeton.edu/BlastO/
16	PHOG	PHOG web server identifies orthologs based on precomputed phylogenetic trees	http://phylogenomics.berkeley.edu/phog/
17	G-NEST	G-NEST is a gene neighborhood scoring tool to identify co-conserved, coexpressed genes	https://github.com/dglemay/G-NEST
18	InPrePPI	InPrePPI predicts protein interactions in prokaryotes based on genomic context	http://inpreppi.biosino.org/InPrePPI/index.jsp
19	STRING	STRING database includes protein interactions containing both physical and functional associations	http://string.embl.de
20	MirrorTree	The MirrorTree allows graphical and interactive study of the coevolution of two protein families and asseses their interactions in a taxonomic context	http://csbg.cnb.csic.es/mtserver/
21	TSEMA	TSEMA predicts the interaction between two families of proteins based on Monte Carlo approach	http://tsema.bioinfo.cnio.es/