Question: how to identify Protein Complexes based on PDB?
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gravatar for Mo
3.4 years ago by
Mo890
/
Mo890 wrote:

Hello,

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

Thanks

proteomics • 1.2k views
ADD COMMENTlink modified 10 months ago by RamRS22k • written 3.4 years ago by Mo890

Complex as in "biological unit"?

ADD REPLYlink written 3.4 years ago by genomax70k

@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

ADD REPLYlink modified 10 months ago by RamRS22k • written 3.4 years ago by Mo890

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

ADD REPLYlink written 3.4 years ago by genomax70k
0
gravatar for Khader Shameer
3.4 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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

ADD COMMENTlink modified 10 months ago by RamRS22k • written 3.4 years ago by Khader Shameer18k

@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 :-)

ADD REPLYlink modified 10 months ago by RamRS22k • written 3.4 years ago by Mo890
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CORUM site has the complexes available for download as a flat file. The link is on the main page.

ADD REPLYlink modified 10 months ago by RamRS22k • written 3.4 years ago by genomax70k

@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

ADD REPLYlink modified 10 months ago by RamRS22k • written 3.4 years ago by Mo890
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