Inferring Protein Domains Interactions
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11.7 years ago
User 0063 ▴ 240

Hi all,

I've a set of protein domains sequences. (homolog proteins) I'd like to infer their interactions? Could you give me any suggestion?

Best regards

protein domain interaction prediction • 2.3k views
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11.7 years ago

It's not that clear what you are trying to achieve. For inferring protein-protein interactions, I would use STRING. For inferring protein domain-domain interactions I would use DOMINE although you would need to annotate your sequences with Pfam first.

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I've selected domain by InterproScan. I'd like to infer domain-domain interactions

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DOMINE also accepts InterPro IDs.

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11.7 years ago
Rm 8.2k

Go through this paper and their software: RCDP , I think its part of DOMINE:

Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions

InterPare; Paper: A protein domain interaction interface database

InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE).

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11.7 years ago
Bilouweb ★ 1.1k

I think this article can also be useful :

Martin Weigta, Robert A. Whitea, Hendrik Szurmantc, James A. Hochc, and Terence Hwaa. Identification of direct residue contacts in protein–protein interaction by message passing

http://www.pnas.org/content/early/2008/12/30/0805923106.short

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