dyMEAN

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Unit in the openmm_relax function

1

Hi, It seems that the openmm's Simulation.minimizeEnergy() method has a default unit set to **kilojoule/model**, while **kilocalories_per_mole** was used at the beginning of the openmm_relax function in the script [relax....

TangYiChing

/delta G scorer code

2

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

Yaoyaolingbro

antibody binding inside structure of the target

1

Hi I love the tool! But i am having some trouble with my antibody and the produced design being inside of the target. Do you have any advice for this?

keithgmitchell

Difficulty Replicating Antibody Optimization Results

1

I've been trying to replicate the antibody optimization results detailed in the paper, strictly adhering to the provided instructions and ensuring the activation of OpenMM relaxation. However, my attempts to...

benyaminjami

It seems that this tool generates a CDRH3 region with a high likelihood of containing many Gs.

1

 What could possibly cause this phenomenon in the CDRH3 region?

semal

Reproducing dyMEAN model in Fig. 4

1

Hi, great work! I was trying to reproduce the dyMEAN model for PDB-ID 1ic7 as shown in Figure 4. However, the models I get do not seem to be positioned...

bud-graziano

Revised codes for no toxin chains, Manual epitope design

3

Excellent work, I tried to generate antibody for COVID NP protein. So, I revised the code as below; if __name__ == '__main__': ckpt = './checkpoints/cdrh3_design.ckpt' root_dir = './demos/data' pdbs =...

Hyeongsun

a formula in paper

1

The two terms on the right-hand side of the formula are the same. How should this be understood?Is this an input error?

semal

Nanobodies

1

Thank you for the code. Can it also work on nanobodies? Thank you

floeshak

Is it possible to use a predicted antibody structure to initialize X_i^(0)?

1

Excellent work, and very thx for open source. This is my question. If Using tools like Igfold or alphafold to predict antibody, then use this structure to initialize X. Of...

semal