I have a list a several proteins and I want to search for interactions between them directly by a second or third protein. Which are the more suitable tools to do this? I've used Cytoscape for already generated networks and I want generate a network with these proteins.
Thanks in advance
You could query your protein list against the BioGrid web site
BioGrid would be the way to go if you are looking for a curated database with experimental data. STRING is more for prediction of functional linkages based on criteria such as gene vicinity, gene cooccurence (phylogenetic profile), data mining... Another similar resource is the Pro-Links website which is mostly for prokaryotes.
http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp
If your data are human, HPRD is suitable.
IntAct, DIP, BIND, iHOP, MIPS, MINT etc, they are physical protein interaction. you can also use of functional interaction
Article Discerning molecular interactions: A comprehensive review on...
Please have a look for the databases useful for interaction network data curation and tools used for network analysis.
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