Sampling from the protein data bank.
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4.7 years ago

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

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

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4.7 years ago

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.

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