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### Issue summary
Hi, I am trying to use GNINA for docking of macrocycles. However no matter if I use autobot_lig command and after the ligand extracted from the protein, or I enter xyz coordinates e…
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this is a fun one, here's the error:
```
Traceback (most recent call last):
File "/home/paynea/miniforge3/envs/asapdiscovery/bin/asap-docking", line 8, in
sys.exit(docking())
File "/lila…
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Hi,
I try to simulate a protein-protein docking between two proteions, one is a mulimer membrane protein which need to be restrained(chain A-I), another is a ligand protein which need move freely, …
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~/AutoDock-GPU-develop$ ./bin/autodock_gpu_128wi --ffile ./input/1stp/derived/1stp_protein.maps.fld --filelist ./input/1stp/derived/ligand.txt
AutoDock-GPU version: v1.5-release
Error: Can't open …
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Hello,
I was wondering if I can use AutoDock-Vina for docking between proteins and peptides.If not, do you have other suggestions?
Best Regards
Soodabeh
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In the Uni-Mol paper, the average number of seconds per ligand is 0.2.
> Efficiency benchmark We compare Uni-Mol binding pose prediction with popular docking tools in efficiency. The baseline result…
tsa87 updated
8 months ago
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It seems that LightDock is capable of protein-protein, protein-peptide and protein-DNA docking. It is not suitable for small-molecule docking (in my case, I was interested in docking a DNA dopamine-sp…
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Hi!
Thank you for your selfless open-source contribution, I have two questions.
How to give a name to a compound based on input ligand.csv instead of index+number in results.
If I want to dock…
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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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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…