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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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The first process of train VAE was successful.
But an error occurred when train_ligand_binging_model.
polygon train_ligand_binding_model --uniprot_id Q9Y572O --binding_db_path /home/yanbosmu/Bioin…
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**Appreciate your outstanding work!**
I'm trying to dock a ligand composed of multiple monomers with my target protein. I set **Molecule Type** to '**ligand**' and **Copies** to 10, but the result …
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Hi,
I tried your pipeline several times but I never get to the end because no files are left.
I first tried the notebook as is, but then I had to change filter values such as SASA_limit when anayl…
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When I used boltz-1 to predict the structure of a protein-ligand complex, the protein structure is fine, but the ligand pose is very distorted and rather remote from the pose in a reference x-ray crys…
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I am using AutoVina for multi-ligand docking and encountered an issue related to the binding energy scores. A fter performing a multi-ligand docking run, I extracted each ligand from the complex and c…
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Hello, I am using Vina version 1.2.5 to process docking of multiple phenolic acid compounds and enzymes. I have encountered the following problems and would appreciate answers!
1. both active site 1 …
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- a small ligands dataset
- a pair of binding sites
- example commands showing how to use those
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Hi
my name is jong hui hong
while I'm trying to train 3d CNN with my data, I got problem with
grid box size because my ligand was too big.
I know that the size of grid box which encompass
pro…
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Hi can I ask you about get_interaction_label for ligand. Do you treat this label as the feature of each node(atom) or not?
Do predict ligand conformation also have significant in binding with interac…