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generatebio / chroma

A generative model for programmable protein design
Apache License 2.0
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Prediction of secondary structure #38

Closed ahof1704 closed 5 months ago

ahof1704 commented 5 months ago

Hi,

In figures 5g and 5h of your paper, you indicate that Chroma can predict the alpha and beta content of the generated molecules. Could you indicate the code you use for this prediction?

Thanks Antonio

wujiewang commented 5 months ago

Thanks for the question, you can just use the log likelihood from ProClassConditioner for the content probability. It is a trained model for conditioning.

But you just use any DSSP programs (e.g. https://github.com/ShintaroMinami/PyDSSP ) to compute secondary structure contents, which will be more accurate.

wujiewang commented 5 months ago

closing this issue for now. feel free to reopen or submit a new issue if you have follow-up questions.