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Thank you for open-sourcing your work; I have learned a lot from it. I currently have my own protein-ligand structure and would like to use D3FG to generate molecules. Could you please guide me on how…
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Thanks for you opening our source code and the fantastic works.
I have a few questions I’d like to ask.
Firstly, the protein-ligand complexes in MISATO likely come primarily from the PDBbind dat…
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This software is very impressive!
Is it possible to add a feature for direct upload of PDB files or ligand sdf/mol2 files for protein-ligand binding prediction or protein-proterin binding prediction…
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Thanks for you opening our source code and the fantastic works.
I have a few questions I’d like to ask.
Firstly, the protein-ligand complexes in MISATO likely come primarily from the PDBbind dat…
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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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**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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One protein (230 aa) plus ligand (phospholipid, ccdCodes = ["PCW"])
With one phospholipid, ligand structure is good and phospholipid (C18) found its way in the binding site with a reasonable orient…
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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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Dear BFEE2 team,
I am using BFEE2 to determine the binding energy between two large proteins (~150 amino acids for the ‘ligand’ and ~400 amino acids for the ‘protein’, respectively). I am using the…
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I wish to perform a docking simulation involving a single ligand and a single protein. And then use this code in 'https://github.com/deepmodeling/Uni-Mol/tree/main/unimol'
`nthreads=20 # Num of th…