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THUNLP-MT / dyMEAN

This repo contains the codes for our paper "End-to-End Full-Atom Antibody Design"
https://arxiv.org/abs/2302.00203
MIT License
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/delta G scorer code #19

Open Yaoyaolingbro opened 5 months ago

Yaoyaolingbro commented 5 months ago

How can I singly run the /delta G scorer code? or where is it? (If I can extract it)

kxz18 commented 5 months ago

We have provided two methods to score ddG instead of dG. One is through an end-to-end deep neural network, the codes of which is here and depend on the modules here. Another one uses foldx to predict dG of the wild type and the mutant, and calculate the difference as ddG. The codes for using foldx is here, but you need to first download the executable binary of foldx from its official website. Also, it is recommended to first use openmm to relax the structure, and then use foldx to optimize the structural energy.

Yaoyaolingbro commented 4 months ago

Thanks for your patient reply!