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Hello,
I am encountering an issue when using molpc2 to predict the structure of large proteins with known stoichiometry information. For example, when I try to predict the structure of 1A8R (or 5BSE)…
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Hi,
Is there a way (or a flag) for having multiple PDB structures predicted for protein-protein complex with small molecule? The default is only one outout PDB given.
mtahe updated
1 month ago
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Pdb uses PROMOTIF, we shoud use the same.
see https://www.rcsb.org/sequence/4ro1
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The requirements could be:
- Loading pdb structures - ideally from a remote server and not locally
- Ability to interact with the structure (panning, zooming, etc.) - Ideally the interaction should …
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I have been trying to prep a local folder of 56 structures using the CLI via ` asap-prep --target SARS-CoV-2-Mac1 --structure-dir SARS2_Nsp3_Mac1_main --save-to-cache --cache-dir mac1-prepped --output…
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I'm using OpenMM to build and simulate a protein-ligand system constructed from protein PDB and ligand SDF files.
The results are saved as minimised solvated structure in PDB file and trajectory in X…
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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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Hi,
Excellent work! I am reading ProtSSN and trying to use it, but I have a few questions:
1) The input in downstream tasks is the entire protein, while the training set uses CATH domains. How do…
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Is it possible to use proteins you have generated outside of VirClust?
If so what format/structure should they be?
Thanks
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Explore integrating Alphafold cross-referencing and 3D structures of proteins not in PDB