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dauparas / ProteinMPNN

Code for the ProteinMPNN paper
MIT License
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Sampling temperature for flexible chains #104

Open Davood-Norouzi opened 3 months ago

Davood-Norouzi commented 3 months ago

Hi

Thanks for the great tool!

I am trying to optimize a rather flexible and DNA-interacting protein with ProteinMPNN.

Q1: Is ProteinMPNN a good tool to optimize a protein with moving parts? Q2: I get long stretches of KKKKKs when I do optimization. How to fix that? What is a good value for sampling temperature to avoid this problem? Q3: Do you recommend optimizing for flexible loops in the protein or I better not change those parts? In the paper it is mentioned that ProteinMPNN is good for stabilizing the structure? Does it mean it rigidifies the protein?

Thank you, -Davood