predict possible protein protein interaction - (Feb/20/2012 )
i just want to ask if there is a software or preliminary step to check if there is a possibility for two proteins to interact before i verify it by pulldown or IP or in-vitro binding? i wanted to have a general idea first if there is a possibility for these two proteins to interact. my candidate is a receptor that can shuttle from cytoplasm to nucleus and the other is a transcription factor that can be phosphorylated and also translocate to nucleus.
I understand what you are asking, and the best tools I can think of are these:
Go to the ncbi gene page for your two proteins. Search for the gene name here: http://www.ncbi.nlm.nih.gov/gene
and scroll down to see the grid of interacting partners. These will be the published interacting partners for your proteins.
Also, you can use Pfam to determine what conserved domains are present on your proteins and then read to descriptions of the domains to see if these domains are known to bind certain sequences that might be present on the other protein.