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## Environment Information
Open Babel version: 3.1.0
Operating system and version: windows 11 running ubuntu in WSL running Anaconda3
## Expected Behavior
I am running the script prepareCova…
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Hi all,
I'm trying to perform a covalent docking on a LYS using as worhead a benzenesulfonyl fluoride in which the LYS should do a SN2 on the fluoride bonding with the S (e.g. `FS(=O)(=O)[#6]-1=[#6]-…
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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…
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Scripts:
```bash
Unidock --receptor 1ipb_protein_only.pdbqt \
--ligand_index ligands.idx \
--reference ligands/M7G.sdf \
--scoring vina \
--center_x 10.671 \
…
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Hallo all,
Let's say that I have a protein to which I would like to dock multiple different proteins but always in a 1:1 ratio.
there is a way to provide a list in the fasta file so that the first…
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During Vina flexible docking ligands are getting break .I have used vina_split command to split binding poses .I am attaching screenshots of same for your reference, can you help for same.
Ligand-->
…
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We I run python train_bfn.py --test_only --no_wandb --ckpt_path ./checkpoints/last.ckpt I have this issue:
/users/PCON0041/yufei/.conda/envs/bfn/lib/python3.9/site-packages/pkg_resources/__init__.p…
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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…
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Hi, I used rfaa to test the posebuster set, but the precision I got was not as good as the 42% docking success rate mentioned in the article. I think my test protocol is not consistent with yours. Cou…
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Firstly, thank you very much for attempting to simplify the workflow for those who are not computational biologists.
This is the specific excerpt that the title is referring to:
` python prepare…