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I have some questions that came up when going through the PLB:
1. in some datasets, some of the ligands are deposited more than ones, but they have the same name in the .sdf . It would be helpful t…
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Hi, possibly a very dumb question here, but I was running through the T4-lysozyme / p-xylene example, and I noticed that when I load the receptor PDB and ligand mol2 simultaneously in PyMol, the ligan…
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I am attempting to perform binding site LigandMPNN design on an existing protein small molecule complex (skipping the backbone design step) . I generated this complex by aligning a new ligand into the…
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How about creating a BindingDB dataset, or a BindingDB-minus-ChEMBL dataset?
The BindingDB protein-ligand dataset includes the relevant data from ChEMBL, but also hundreds of thousands of measure…
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Hi,here
I want to reproduce the performance of ACNN in protein-ligand binding affinity, but I can't find the pre-trained model.How can I obtain the .pth file for ACNN? Thanks for your reply.
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We want to see an allosteric conformational change in our complex for a 10 to 15 millisecond time scale frame. We have plans to make the system hybrid. Water and membrane will have a coarse grain, pr…
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First, thank you for your excellent research.
Based on your research, I attempted to predict protein-ligand structures (a kind of binding mode analysis) using single protein:single ligand combination…
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HelloProfessor,
What I am trying to do is separate a small DNA fragment from the binding pocket of a protein and plot the free energy path. Should I use BFEE for this purpose, considering a DNA mole…
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Hello, I am using your pipeline to design hemoglobin binding protein. When I run the code segment "Analyzing diffusion outputs," I encounter the following error. Thank you very much for your help.
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**Aim:**
This issue addresses how to apply LigGrep to filter through docked ligand poses to check that they retain key interactions with the protein that are observed in crystallographic fragment-p…