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output_monkey_uniprot_pdbfiles folder is corrupted
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Hi author,
Right now I download the pretrain weight from [Multiview Contrast](https://zenodo.org/record/7593637/files/mc_gearnet_edge.pth). I want to load this weight, and then pass a pdb file to the…
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Protein structures in NGLview could be colored by their quality, eg. red for homology models and silver for experimental models. This gives a quick idea on the quality of information being presented. …
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The score structures stage (stage 6) generates `structure_scores` files and `all_fragment_scores/frag_scores` files. Per the README and reading some of the closed github issues, the recommendation to …
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Hi,
I was checking ESM-3 structure embedding, and ESM-3 sequence embedding, and found that the distance between embeddings is very less ( 0.0001) . I am curious how ESM-3 model is pre-trained with …
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https://doi.org/10.1038/nature11503
>The genome-wide identification of pairs of interacting proteins is an important step in the elucidation of cell regulatory mechanisms1, 2. Much of our present kno…
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Please add the following paragraph to the [Preferred file formats](https://datadryad.org/stash/requirements#:~:text=the%20Dryad%20DOI.-,Preferred%20file%20formats,-Most%20types%20of) section of our He…
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It might be a silly question but I still don‘t understand how you perform domain clustering by foldseek.
You mentioned in your nature article "Clustering predicted structures at the scale of the kno…
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### Bug summary
In the [ molecules ] section of the topology file, if ions such as "SOD" and "CLA" are placed before the ligand, the function parmed.gromacs.GromacsTopologyFile cannot correctly proce…
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## Correction here
### **C-terminus** was truncated, not. central domain. check Joe's reply in https://github.com/opensourceantibiotics/murligase/issues/36 but does not influence the logic of the ide…