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A generally applicable allowed structure generator could be constructed to streamline code and remove duplicate sections, as well as prevent unnecessary calculations of illegal protein structures. It …
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Hello
I used the easy-search function against the AlphaFold database with the exhaustive search metrics and I noticed my results were greatly conflated where I would have the same protein ID hit mult…
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The conservation pipeline falls down when it runs on modified amino acids. Currently, DODO cannot process modified amino acids. Although the .pdbqt is generated and the docking is done, for the conser…
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We need a set of instructions for reviewers of submitted inputs
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Which is the code to extract features from PDB file and process it with ResNet50? I'm a bit confused and don't know which script it is
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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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Hello Zaixi,
I've read your paper entitled "Full-Atom Protein Pocket Design via Iterative Refinement" and thought it was an excellent way to de novo generate protein structures given a ligand of in…
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Pose a question about one of the following articles:
“[Human-level control through deep reinforcement learning](https://www.nature.com/articles/nature14236)” 2015. V. Mnih...D. Hassabis. Nature 51…
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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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### Operating System
Windows
### Version
2.1.0
### Python Version (optional)
3.10.12
### Python Virtual Environment
Not using a virtual environment
### Execution Environment
Local environment…