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Hi! I am trying to generate molecules based on MTOR and MEK1 as written in the Github repo, but I am missing the `ligand_smiles.txt` for both protein, as stated in the `scoring_definition.csv`. Are bo…
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Host-guest/protein ligand binding data: Do we use host-guest/protein-ligand data in our fitting? Or just for benchmarking? If so, which systems should we look at?
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Dear Dr Judemir Ribeiro,
I'm pretty interested in your recently published tool dr-sasa, which can be used to calculate solvent-accessible surface area (SASA).
In my study, I want to calculat…
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## Is Your Feature Request Related to a Problem? Please Describe.
using the obsidian-citation plugin and Better BibLatex export, I would like the frontmatter under the the {{keywords}} (technically…
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Either the ligand or apo-protein coordinates are centered and the other is not. I believe the protein is (0,0) centered and the ligand is centered in quadrant one. Need to translate the ligand back to…
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Hello,
I really enjoyed the paper and am trying to implement this method to score several novel protein-ligand interactions that are not part of the training data. I have trained the model and am n…
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In the Uni-Mol paper, the average number of seconds per ligand is 0.2.
> Efficiency benchmark We compare Uni-Mol binding pose prediction with popular docking tools in efficiency. The baseline result…
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## *Repository Creation Request*
1. #### Coordinating Institute: Indian Institute of Technology Kharagpur
2. #### Approved Proposal: [Experimental Biochemistry](https://drive.google.com/file/…
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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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Hi author,
Huge fan of your work. I am currently trying to apply your code to a downstream task. Specifically, I am working with a protein PDB file and aim to extract the latent representation of the…