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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?
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14 months ago

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.

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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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21 months ago
European Union

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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