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Hi,
I am trying to design a Lysine Binding Protein using LigandMPNN, but it seems that my ligand, which is lysine, is not being recognized. Could you please explain how LigandMPNN considers ligands…
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If my protein does not belong to an explicit pfam family, how to generate a new sequence?
I guess: extract the closest pfam family(or several families) to fine-tuning the progen2 pretrained model, ri…
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I tried to use your pipeline. in the [Analyzing diffusion outputs] section of 0diffusion, the following error occurs. I tried to use your 7o2g_HBA.pdb with small molecule HBA and it works fine, I don'…
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Running the following command:
```bash
python run.py \
--model_type "ligand_mpnn" \
--seed 111 \
--pdb_path "./inputs/1BC8.pdb" \
--out_folder "./outputs/sc_defau…
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SIB curators are moving from free text annotation describing the effects of variation on protein structure and function, e.g. "reduces protein stability", "interferes with zinc binding". They have fig…
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Hi, I want to build a protein-ligand system where the ligand has more than 150 atoms.
Here is my script:
```
def read protein(protein_file):
protein = pdbfile.PDBFile(protein_file)
retu…
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Hello Zaixi,
I've read your paper entitled "Full-Atom Protein Pocket Design via Iterative Refinement" and thought it was an excellent way to de novo generate protein structures given a ligand of in…
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runfile('/Users/hmh2017/Downloads/neurips19-graph-protein-design-master/experiments/train_s2s.py', wdir='/Users/hmh2017/Downloads/neurips19-graph-protein-design-master/experiments')
Number of paramet…
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[MurD_generative_modelling_TCS.pdf](https://github.com/opensourceantibiotics/murligase/files/8797342/MurD_generative_modelling_TCS.pdf)
We have designed few molecules against allosteric site of MurD …
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Hi, I'm curious if DEqMS allows for the possibility of fine tuning the linear mixed model that it runs on each protein. Basically, my problem is that I am working with samples from a wild population …