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* Could use docking of insecticides in P450s as an example. Assess impact of amino acid changes.
* Or F120…
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Our current workflow is to align conformers by selected atoms and minimize to reduce clashes. Another workflow could be to filter poses from molecular docking keep conformers where the RMSD of selecte…
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"Docking" used to be a Topic (EDAM 1.12) but was deprecated, and merged into the notion of [Molecular modeling](http://edamontology.org/topic_2275). Yet it's suggested as a topic in https://github.co…
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Thanks for your interesting work!
Can you provide more details about the docking protocols of the molecular docking software mentioned in your paper (e.g. Autodock Vina, Vinardo, Smina)? I would like…
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### Virtual library cleaning: Removing Boc-, Fmoc-, and tbutyl ester- protecting groups from molecule libraries.
The Python script [deprotect.py](https://github.com/user-attachments/files/1750667…
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### Issue summary
Docking simulation was performed using vina and gnina, respectively.
Next, we calculated the RMSD of the template and simulation results using the TOOL provided by “The Yang Zhan…
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I have some "flexible" molecules obtained from crystal structures or DFT calculations, and I want to use aISS to generate aggregate structures for them. When directly using the default aISS process, I…
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https://arxiv.org/abs/2210.01776
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[Hou, Tingjun, Junmei Wang, Youyong Li, and Wei Wang. “Assessing the Performance of the Molecular Mechanics/Poisson Boltzmann Surface Area and Molecular Mechanics/Generalized Born Surface Area Methods…
cramg updated
3 years ago
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Here we will accept molecule design suggestions from the public (provided a score below -5.2 kcal/mol) to see if any improved Vina binding scores can be found at the C-terminus-B pocket.
A three-p…