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After creating environment and all the dependencies the final command line python3 -m inference.py --config default_inference_args.yaml --protein_ligand_csv data/protein_ligand_example_csv.csv --out_d…
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I followed the posebuster.ipynb provided in your repo, downloaded the weight file and downloaded the eval_set zip files. However, since the eval_set does not contain pdb file, so I downloaded from the…
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Our partners at the Univ. Kansas have successfully produced Pf CLK1 and PKA-R in milligram quantities for ligand binding and structural studies. We previously predicted these two proteins as the most …
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Hi,
I was recently introduced to PLIP in order to find all interacting Amino Acid residues between a protein and a ligand (PDBQT files that are within .tar collections). I ran these docking throug…
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I would like to ask if Vina-GPU-2.0 can perform Multiple ligands docking like Vina? if Yes, how to write the config file or submit the job?
I have tried to do it like Vina:
Vina-GPU2.0+ --config co…
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Hi!
In [https://github.com/ccsb-scripps/AutoDock-Vina/issues/80#issuecomment-1019534197]
As mentioned in the link, it seems that autodock-gpu can already do covalent docking, but I don't know how to…
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Hi,
I was wondering if I could use AutoDock Vina scoring functions to evaluate protein-peptide complexes.
I used Python-based scripts from the AutoDock Vina website just for scoring the complexes.…
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Hi,
Recently I tried a file of a few thousands of molecules, and found that ODDT keeps getting stuck and idle halfway through. I would appreciate it if you could look into the problem.
Thanks.
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In this project, the main key is to find the binding site of the WDR 91 protein. In order to do this, I have decided to delete the ligand from the [8SHJ](https://www.rcsb.org/structure/8SHJ) and decid…
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For example "within( 3, 12:A )" to select all atoms with 3 angstrom of residue number 12 in chain A. Depends on fast distance calculations (#76).
arose updated
5 years ago