-
From the log file:
```
2023-12-13 12:31:55,112 | root | INFO | cross_docking.py | cross_docking_workflow | Loaded 1 query ligands
2023-12-13 12:31:55,115 | root | INFO | cross_docking.py | cross_do…
-
"Docking" used to be a Topic (EDAM 1.12) but was deprecated, and merged into the notion of [Molecular modeling](http://edamontology.org/topic_2275). Yet it's suggested as a topic in https://github.co…
-
Hi Everyone. Whenever I try to save embeddings for my protein sequence I get an error suggesting nothing is returned from running the model.
Running the multimer model on a protein complex (in csv…
-
For some applications, such as protein-RNA complexes, I'd like to pair sequences by a custom method- and input already paired seqs (2 alignments where sequence X in ali 1 is paired with sequence X in …
-
When calling `omnipath.requests.Complexes.complex_genes()`, the `references` column always reports stripped references which, in turn, results in the `references_stripped` column containing rubbish da…
-
I am trying to get some predictions of protein-protein complexes.
As "positive" control, I use prediction for a complex for which the cryoEM structure was solved and published in second half of 2022.…
-
Is it possible to use the software for the calculation of energy differences between a WT monomer and a mutated monomer, both of them are not a complex, so I cannot define a ligand and receptor. I hav…
-
This might be true for a few different examples, but if I try:
```
asap-docking cross-docking --ligands input/lig_0.smi --pdb-file input/NP_722463.1_lig_0.pdb --target ZIKV-NS2B-NS3pro --cache-dir p…
-
I executed the following command in a container created from the provided Dockerfile:
```bash
micromamba run -n diffdock python -m inference --config default_inference_args.yaml --protein_ligand_c…
-
Jacky Hayles has annotated a number of cell cycle papers that I have been putting off because of the unavailability of the correct cyclin-dependent kinase complexes.
I think we decided a while a…