Downloading non redundant pdb structure files
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Entering edit mode
15 months ago
vipul.iitd12 ▴ 10

Hi, I am trying to download high resolution protein structure files with minimum redundancy in the sequence. So i want the files to have unique sequences. Earlier there used to be an option to set redundancy (e.g. 90 percent and so on) while downloading files in bulk on RCSB website but now i can’t find the option. Can someone please suggest some alternative.

Thanks in advance Regards Vipul

pdb non redundant rcsb python protein • 937 views
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Entering edit mode
14 months ago
jgreener ▴ 380

I couldn't find the option either so I made a help request and was pointed to a blog (https://www.rcsb.org/news?year=2020&article=5e8e747dd6224512994720f1) that says:

Please note some RCSB PDB features are still in development but will be made available soon, including Custom Tabular Reports, Chemical Component Search tool, sequence motif search, access to SDF files, and others.

In the mean time you could use something like BLASTClust.

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14 months ago
Mensur Dlakic ★ 14k

PISCES should do the trick. You can use one of their many pre-compiled lists, or create your own list by setting custom resolution and R-factor criteria.

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