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I am only focusing on the standard runs of `-mm 5` and `-mm 6` for two monomeric protein structures. I want to remove all extraneous parameters that are currently implemented in USalign's code base (i…
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The protein-small molecule complex generated by RFAA has numerous clashes, and even after energy minimization with Schrodinger, there are still many clashes. Does this mean that the resulting structur…
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Traceback (most recent call last):
File "/opt/conda/bin/run_structure_prediction.py", line 274, in
app.run(main)
File "/opt/conda/lib/python3.10/site-packages/absl/app.py", line 308, in ru…
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This is not a bug but rather a request that, however, I am sure everybody will stand by: please add a way to specify in the input json file what is the number of the starting residue of each chain.
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## Context
I need to create MSAs for a very large set of protein sequences: about 25 million.
I was planning to use the ColabFold workflow. I figured that this would be achievable given the nonlin…
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**Youtube**
- [x] [AlphaFold2, OpenFold, Protein Language Models and Beyond | Nazim Bouatta](https://www.youtube.com/watch?v=ON1ltprZKPo) from Molecular Modeling and Drug Discovery (M2D2) 2022
- […
kntkb updated
10 months ago
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I installed localcolabfold and copied HighFold git repo into my localcolabfold.
So that my localcolabfold git repo looks as
![Screenshot 2024-06-25 at 5 29 04 PM](https://github.com/hongliangduan/…
kimdn updated
4 weeks ago
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Hi, I love your work and the possibilities that offer being superfast. I was wondering if is it possible in binder design to only design specific residues of the binder knowing the structure of the ot…
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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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https://doi.org/10.1101/137828
> Understanding the relationship between protein structure and function is a fundamental problem in protein science. Given a protein of unknown function, fast identif…