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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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Automatic Repair of missing PDB coordinates #457

Open fgrunewald opened 1 year ago

fgrunewald commented 1 year ago

Here is a webserver which also has a pypi package that is separately install able. It repairs protein pdbs adding missing atoms etc.

https://pypi.org/project/Pras-Server/

Like with the proPka we could use it to clean the input PDB. I tried the webversion on a moderately big protein and it works quite nicely.

Added bonus: It can assign secondary structure with similar accuracy as DSSP without being equally shitty at output. I need to test more but could be a very nice plugin.

pckroon commented 1 year ago

Cool, I like it. It would also add the option of reading mmcif files, which is a big plus.