Question

Sampling from the protein data bank.

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7.8 years ago

underoath006 ▴ 10

I'm looking for a way (pymol, biopython / python script, or whatever) to sample from the entire pdb. I want to select pdb's with a certain attribute, a certain resolution, or rule out a certain attribute, for example membrane proteins. I also want to rule out pdb's that have metal atoms in them.

Any suggestion on how to approach this problem?

Sincerest regards.

pdb pymol python biopython • 1.5k views

ADD COMMENT • link updated 7.8 years ago by Petr Ponomarenko ★ 2.8k • written 7.8 years ago by underoath006 ▴ 10

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Information about PDB's REST API is on this page.

ADD REPLY • link 7.8 years ago by GenoMax 147k

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Thanks, but doesn't have an option for heteroatoms. Any suggestions?

ADD REPLY • link 7.8 years ago by underoath006 ▴ 10

score 0 · Answer 1 · 2017-03-03

Another option is to use ICM Browser and there is a way there to represent all these attributes for all pdb files as atable or for a subset (created as a result of searching for certain fields). A better thing is that you can make your search more detailated and variable. For example instead of having cutoff of 2.5A for GPCR structures you can select top 5% by quality and so on.