Map PDB match coords to Pfam protein domain
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Entering edit mode
6.8 years ago
Anand Rao ▴ 550

I am using hhpred to find matches to my peptide queries (45-50aa long) against the PDB database.

For the matching coords in the top-ranked PDB file, I want to check whether those coords correspond fully or partially to my (Pfam-defined) protein domain of interest.

How can I perform this mapping of PDB match to Pfam domain name in a high-throughput manner at the command line?

I realize there are links to 3rd party tools for parsing the PDB files ( http://bit.ly/1JcsSt6 ), but I've never played around with PDB files, so I thought I might first glean ideas from the helpful forum members here. If you think I could ask this question in another forum more qualified to answer this question, I would appreciate that as well. Thank you!

protein PDB mapping domain • 2.5k views
4
Entering edit mode
6.8 years ago
peter.rose ▴ 110

You can retrieve PFAM assignments using our tabular report RESTful web services.

We run PFAM HMMs to update PFAM assignments.

Example URL with two PDB IDs:

http://www.rcsb.org/pdb/rest/customReport?pdbids=1A0K,1AA2&customReportColumns=pfamAccession,pfamId,pfamDescription&format=csv&service=wsfile

This produces the following .csv file:

structureId,chainId,pfamAccession,pfamId,pfamDescription
"1A0K","A","PF00235 [2-126]","Profilin","Profilin"
"1AA2","A","PF00307 [5-106]","CH","Calponin homology (CH) domain"


If the list of PDB IDs becomes long, you need to use POST rather than GET in the web service call.

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Entering edit mode
6.8 years ago
andreas.prlic ▴ 290

RCSB PDB is scripting the HMMER web serives on a weekly basis and in addiiton to the web-service link posted above, the data is also available from here.

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Entering edit mode
6.8 years ago
Anand Rao ▴ 550

I may have found my answer at http://www.ebi.ac.uk/pdbe/docs/sifts/quick.html

I must cross reference an earlier question here at biostars that elicited numerous answers: Merging Data From Pfam Pdb And Uniprot

I am not sure whether the mapping information is most up to date, but its a really good start for me in any case.