Uniprot Retrieve/ID mapping
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Entering edit mode
6 months ago
jmungar2 ▴ 10

Hello everyone,

I'm trying to map a few thousands of proteins from their pdb codes and chains to Uniprot ID.

I tried this approach (Get Uniprot entry name from PDB ID and chain (solved)) but the url (https://www.rcsb.org/pdb/rest/das/pdb_uniprot_mapping/alignment) has been removed ("It has been permanently removed as part of our announced shutdown on December 9th, 2020").

Does any one know if this mapping database is now accesible on a different url?

I've also tried doing the mapping over the website (https://www.uniprot.org/uploadlists/) but it doesn't allow to specify the chain, so I get the mapping for every chain in each pdb. Also, since the output does not specity the chain corresponding to each result I can't filter them afterwards.

Any ideas?

Thank you Juan

Uniprot Mapping PDB2Uniprot • 292 views
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Entering edit mode
6 months ago
GenoMax 107k

Take a look at the idmapping files UniProt provides in this directory. It may be simpler to just get the data and parse things you need.

It should be possible to do this using new API that UniProt has. You may want to ask UniProt support directly about that.