Protein Protein Interaction Prediction For Orthologue Proteins

Question

[Sudeep]

Hi all, What are the existing methods (stand alone tools) available for protein protein interaction prediction for orthologue proteins ? I know that STRING has some interaction data from homology modeling and I am working on a species with very little interaction data, so I did not have much success with any other databases. For ppi prediction from orthologs I came across this perl module and InteroPorc stand alone tool. But does someone has any other suggestions or experience with such stand alone tools for ppi prediction for orthologs ?

Thank you

Answer 1

[Paul Denny]

Try Perl module described in this paper: "Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161927/?tool=pubmed It accepts as input a list of Ensembl gene accession numbers from any of the vertebrate or metazoan genomes in Ensembl, which includes Bos taurus.

Answer 2

[Khader Shameer]

Homologous pairs of protein interactions across different organisms are called as interologs.

Information about interologs will enable annotation transfer between genomes and may also help to derive evolutionarily conserved interaction modules.

Please check following databases:

• Interolog/Regulog Database
  
• 3D-Interolog Database

[Sudeep]

Thank you (for the articles and databases). Interolog/Regulog Database is only dealing with "model organisms", so I am leaving that out completely.

[Khader Shameer]

What is your organism ?

[Sudeep]

its actually cattle

[Khader Shameer]

That's a vague description for an "organism" name in the context of biological. Can you please give the species/sub-species name ?

[Sudeep]

to define it clearly it is Bos taurus (or commonly cattle)