Downloading non redundant pdb structure files

Question

[vipul.iitd12]

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

Answer 1

[jgreener]

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.

Answer 2

[Mensur Dlakic]

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.