I have a set of proteins of interest from a non-model organism (the beautiful marine bivalve Ruditapes philippinarum) and I would like to "predict" / map possible protein-protein interaction.
Under what conditions can I use STRING networks predicted for different species?
Is there a more appropriate tool for my purpose?
Any help, suggestions, comments and criticism is very welcome!
You can also use Visant for visualise protein-protein interactions.
be certain that you have homologous proteins in the different species studied (BLAST, protein domain, NCBI homologene database could help you if your proteins are in genebank, ...)
Thanks Aurélien I will check it out.
Btw I also posted the question on Biostars.org, where it was suggested to start by inferring orthologs of my proteins of interest in a model organisms (e.g. using TreeFam). The complete answer can be found here:
https://www.biostars.org/p/147569/
You can also try IntAct from EBI.
http://www.ebi.ac.uk/intact/
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