An example demonstrating PSSM biasing

dauparas / ProteinMPNN

Code for the ProteinMPNN paper

MIT License

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An example demonstrating PSSM biasing #6

Closed GeneMachines closed 1 year ago

GeneMachines commented 2 years ago

I'm having a little trouble getting the code to run with a PSSM as input. I'm also not 100% sure how PSSM biasing is influenced by the pssm_multi, pssm_threshold, pssm_log_odds_flag, and pssm_bias_flag flags. It would be great to have an example with input files and flag usage when including a PSSM.

Thanks!

Gordon5-AI commented 2 years ago

Same questions, this work has been done very well, but the specific meaning of some parameters is not detailed enough. It will be more helpful if you can provide a detailed tutorial later. Thanks!

donglg1309 commented 1 year ago

The PSSM flags are confusing based on the current version. A further PSSM help script will be helpful. It seems that the file '/home/swang523/RLcage/capsid/monomersfordesign/8-16-21/pssm_rainity_final_8-16-21_int/build_0.2089_0.98_0.4653_19_2.00_0.005745.pssm' cannot be accessed.

Thanks!

dauparas commented 1 year ago

Sorry, I forgot to paste this example here: https://github.com/dauparas/ProteinMPNN/blob/main/examples/submit_example_pssm.sh I hope this helps!