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Given a list of cell surface genes, is there a computational possibility to predict their interaction partners on the surface of another cell?

Hi folks. After performing differential expression analyses on my single cell RNA sequencing data from ILC2s of mouse origin, treated under three conditions, I generated a list of differentially genes. I afterwards used the Gene Ontology platform to generate a shorter list of genes proven to be present on the surface of mouse cells. Is there a computational possibilty to predict interaction partners of these ILC2 surface genes present on the surface of mouse fibroblast cells?

Thank you in advance for your help.

gene rna-seq r fibroblasts geneontology
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updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by charlesgwellem • charlesgwellem

1)This is not exactly what you asked for, but I've found a pdf-file describing molecular docking

and a lot of tools to work with it. http://caps.ncbs.res.in/download/mmpli_talks/Softwares_for_Molecular_Docking.pdf

It's from 2007, some soft may not exist any more, but it's worth looking at, I think.

2)There is another article of virus-receptor binding, https://peerj.com/articles/266.pdf

It mentions some computational tools as well.

3) There is a large drug-design database.

Directory of computer-aided Drug Design tools:

http://www.click2drug.org/

4) Cell-surface human proteins, a post from biostars:

Database of human genes encoding cell surface proteins

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written by natasha.sernova natasha.sernova

1 answer

I do not think so. The best approach I have seen was this paper whether they use a currated list of receptor-ligant interactions (available here) and tried using the expression of those pairs. But to my knowledge no computational tool.

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written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

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