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Related to #247 - currently Yank has systembuilder, which probably ought to be split off into a more general-purpose tool that will be useful aside from just for Yank workflows (i.e. setup of GROMACS …
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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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Hello, may I ask if it's possible to ensure the interaction of certain key amino acid residues during the docking process?
In fact, we need to dock a series of analogs to further determine which c…
TVect updated
5 months ago
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### Issue summary
### Steps to reproduce
Dear developer,
I am a beginner in this area and have tested using examples in [example colab notebook](https://colab.research.google.com/drive/1QYo5Q…
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Hi all!
This issue can be viewed in isolation / together with the other Issues I've created so far:
Issue #30 : Characterisation of the 2D protein-ligand interaction map
Issue #31 : Making a mole…
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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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The recent [brilliant results](https://github.com/OpenSourceMalaria/Series3/issues/14#issuecomment-605044400) have identified OSM-S-106 as a potent inhibitor of PfηCA (Ki of 2.2 nM ) with useful selec…
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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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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…