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brennanaba / PLAbDab

The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures
BSD 3-Clause "New" or "Revised" License
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Database with url integrated #8

Closed immunomotivees closed 5 months ago

immunomotivees commented 5 months ago

Hello,

Thank you very much for this database, it is very helpful ! I saw in util.py that you build the function add_url_to_paired_data(df) but do you have any database that is already filled with these informations ?

Furthermore do you have any insight on how to retrieve target sequences based on information from paired_sequences.csv ?

Thanks for any insight you can provide Best regards, Celia

brennanaba commented 5 months ago

Hi Celia,

Thanks a lot for your kind comments about PLAbDab!!

You can generate a version of the database with urls by doing a search by keyword on the website using an empty keyword.

Unfortunately, I am not aware of a general method to retrieve sequences for the targets. If you have a specific entry in mind, you can probably search for the antigen name in the NCBI protein database: https://www.ncbi.nlm.nih.gov/protein/

I hope that helps!!

All the best,

Brennan

immunomotivees commented 5 months ago

Hello Brennan,

Thank you very much for your answer

Best regards, Celia