how to identify Protein Complexes based on PDB?

Question

[Mo]

Hello,

I would like to know if anyone knows how to identify complex for a list of proteins ID using PDB

Thanks

[GenoMax]

Complex as in "biological unit"?

[Mo]

@genomax2 In any unit you can. I was more interested in CORUM but the problem I could not find a way to do it and I found that one can use PDB as well. that is the main reason I asked

[GenoMax]

REMARK entries (I think it is REMARK 350) in PDB files include information about biological unit constitution.

Answer 1

[Khader Shameer]

Have you tried 3dcomplex?

I would also recommend looking at CORUM, capturing complexes in 3D/Crystallography is incredibly hard. Affinity/protein-binding based mass-spec experiments and data offers a better coverage for complex data. We have done some complex analyses using Mass-spec data - check our approach here

[Mo]

@Khader Shameer Do you have any R , python, any approach , example, tutorial , how one can do that? I have been busy for this since few days and I am even not close to understand :-)

[GenoMax]

CORUM site has the complexes available for download as a flat file. The link is on the main page.

[Mo]

@genomax2 Yes for sure, but I dont know how to map them, if there is an example, I can follow and get to do it . do you know any example? I have a list of Uniprot protein IDs