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CCBatIIT / Bridgeport

Code for the preparation and running of OpenMM Simulations with the Open Force Field (Requires Python 3.9)
MIT License
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New workflow for filtering docking poses by RMSD of selected atoms #25

Open daveminh opened 2 weeks ago

daveminh commented 2 weeks ago

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 selected atoms is under a specific threshold. This could generate plausible poses more efficiently.

davidcooper7 commented 1 week ago

This issue would require a workflow that navigates around the usage of mgltools to be compatible with the conda environment. I believe @jimtufts has a workflow in place that could be integrated.

jimtufts commented 1 week ago

Ok, yeah I’ll take a look at it.

Jim

From: davidcooper7 @.> Sent: Monday, November 18, 2024 7:01:04 PM To: CCBatIIT/Bridgeport @.> Cc: jimtufts @.>; Mention @.> Subject: Re: [CCBatIIT/Bridgeport] New workflow for filtering docking poses by RMSD of selected atoms (Issue #25)

This issue would require a workflow that navigates around the usage of mgltools to be compatible with the conda environment. I believe @jimtuftshttps://github.com/jimtufts has a workflow in place that could be integrated.

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