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Hi, I run simulation on the following system for a given dimer structure. Whenever I run with different parameter and put into VMD, I see each protein subunit seperate each other and be outside simula…
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Hey!
First of all thank you very much for providing MutateX and also RosettaDDG prediction! I am using RosettaDDG prediction to refine upon my predictions from MutateX and i want to use MutateX for p…
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I followed your method to generate secondary structure sequences for proteins in cafa3 and then performed one-hot encoding on them to create features. However, the prediction performance is not satisf…
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I think we should establish a recommended protocol for preparing protein structure file. The following is more or less what I plan to do while setting up YANK simulations of HSA. Please share your com…
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Hi tfold team,
I applied tFold-ag to the AbDB dataset, and while it performs well on some proteins, I encountered difficulties predicting other proteins. Upon inspecting the predicted structures, …
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I tried to use different ligands to dock with the proteins in the repo .According to the files in your examples, when I tried to dock with 2br1_protein.pdb and 2wtv_protein.pdb, it worked .But when I …
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Since I can run [Predicting Protein Monomers example](https://github.com/baker-laboratory/RoseTTAFold-All-Atom?tab=readme-ov-file#predicting-protein-monomers) well, I tried [Predicting Covalently Modi…
kimdn updated
5 months ago
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Hi
How is it possible to generate a structure database from my own protein structures in order to search with new proteins? I tried to generate new descriptors but it seems this is just for a prot…
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Hello,
I downloaded a protein structure from AlphaFold (PDB) and tried to use PDB2PQR but it gets stuck at "pending job start" for multiple days straight.
Bw
Hillary
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For @mariacm12 `asap-genetics` pipeline we need to have a protein structure prediction pipeline. @hmacdope to investigate.