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For molecules with saturated ring systems (e.g. sugars) it can be useful to implement sampling of initial ring conformations, dock them separately and choose best output. This looks critically importa…
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If you make a spoonerism of PrimaryDock, it sounds like "dimer-y proc". Therefore, by its name, this application must be enhanced to allow docking ligands into dimers, ideally both heterodimers and ho…
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Hi,
I'm interested in capturing the exact state of the receptor after flexible docking.
It seems there is no description about that on docs, but is there any way to do that with vina?
If not…
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What file is this "checklines.txt"? How did you get it?
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### Issue summary
I've been using GNINA and for some compounds in my test set, the bond orders are generated incorrectly, leading to errors when parsing the SDF output using PandasTools.
I've atta…
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Thanks to the authors for their excellent work.
Is it normal to go on for a long time at this step?
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**OS: Windows (V2.1.0)
Linux (PRinS3_V_2_1_0_Ubuntu_2020_64x)**
**Application: X-ESS (Docking)**
**Issue:** For the protein files with missing Hydrogen atoms, Docking Jobs are getting completed …
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[Zoe Cournia, Bryce K. Allen, Thijs Beuming, David A. Pearlman, Brian K. Radak, and Woody Sherman. "Rigorous free energy simulations in virtual screening". *Journal of Chemical Information and Modelin…
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It would be good to have some fleshed out use cases to understand what this file format will (and won't!) support. Here's a brainstormed list that probably reflects my biases:
Biomolecular
- A protei…
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Thank you for putting this repo together, it is really helpful in understanding and preparing the features for AlphaFold. I was wondering if it is possible to include non-covalently-linked ligands alo…