I wanna analyze virus proteins' interaction network with its vector insect proteins. Now I have the virus and insect genome and geneset. Are there some convenient pipelines or software I can use to de novo predict (since there are few known interactions between this virus and its host) the virus-vector protein-protein interaction from a genome scale based on some published databases? I mean tools or softwares based on known interaction and apply some algorithms to de novo predict PPI.
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We have developed an in silico method that can predict protein-protein interaction between any virus/host association based on interology inference see our poster and contact us if interested
1.8 billion Virus/Host ppi infered by interology using @virhostnet2 data. Poster n°35 @Justine_Picarle #JOBIM2016 pic.twitter.com/I0UdsdPE4M
— virhostnet (@virhostnet2) June 27, 2016
Thank you. Have you ever tested on insect-virus interaction and can it be used to predict protein-protein interaction between virus and host de novo?
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I don't know of any methods that do what you want, and I also think it is a tall order just from sequence information. But you should make sure to put an effort in doing a literature search of PPI predictions to see if anything exists that could work for you.
One method that could help you is STRING (http://string-db.org/), but I do not know how reliable it will be for virus-insect interactions.
Thank you. I have been searching for studies about PPI prediction. There are in deed lot of PPI prediction methods, say sequence-based, domain-based or structure-based, etc. Only a few, however, is about virus-human interaction. It's a lack of insect-virus PPI knowledge. I'm sorry that STRING is not really helpful here due to the viral proteins , highly variable and poor database.