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Hi @martin-steinegger ,
Thank you for the awesome software for structure-based clustering and sequence search. I was wondering if its possible to run the `easy-search` or `easy-cluster `commands wi…
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Hello,
As per [this line](https://github.com/aqlaboratory/openfold/blob/main/openfold/model/evoformer.py#L649), when neither Deepspeed nor LMA is selected, the custom memory-efficient [kernel](http…
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Dear OpenFE team.
Thanks for this awesome work.
This is related to https://github.com/OpenFreeEnergy/openfe/issues/633 https://github.com/OpenFreeEnergy/openfe/issues/634 and https://github.com/Open…
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Hi,
I am attempting to utilize ColabFold to predict the 3D structure of a protein dimer connected by a disulfide bridge.
I understand that AlphaFold can accomplish this using the following comma…
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PDB ID: 3AG9
in pymol:
![1719390982893](https://github.com/molstar/molstar/assets/17419987/aa3f27dd-f410-4c77-9ab5-0559587791e0)
in molstar:
![1719391100858](https://github.com/molstar/m…
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Hello!
I have a query concerning a specific aspect of protein-ligand systems. In cases where both the protein and ligand are identical, but the final conformation varies due to sampling of the protei…
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request from @bebatut
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Environment:
GPU: NVIDIA RTX 3060 12GB
PyTorch Version: 2.3.1+cu118
CUDA Version: 11.8
OS: Linux Ubuntu
Python Version: 3.10.13
Amino acid : 651
I am encountering a CUDA Out of Memory erro…
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Background
Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, e…
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Hi there!
How do I do inpainting on a multichain protein? For e.g. I want to make sure that all 3 chains in a trimer get the same changes. In proteinMPNN there is an option of `tied_positions` but …