Author: sargis
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Older Publications Using PyRx
The following are older publications where PyRx has been mentioned. Please let us know if we miss any citation. Thank you all for using PyRx! Exploring common pathogenic association between Epstein Barr virus infection and long-COVID by integrating RNA-Seq and molecular dynamics simulations Kanwal A, Zhang Z. Front Immunol. 2024 Sep 26;15:1435170. Therapeutic potential of…
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COVID Update II
It has been more than 5 months since the last update. Remdesivir first identified in Coronavirus Drug Discovery Competition as a potential COVID-2019 treatment is now authorized for emergency use by FDA. This is the fastest drug I’ve seen to go from ideation to clinical use. Although, given the price and scarcity, I hope, steroids can…
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COVID-19/Coronavirus Update
I’m glad to report that PyRx has been used to win Coronavirus Drug Discovery Competition. Congratulations and HUGE THANK YOU to Matt O’Connor who used deep learning techniques for molecule generation and PyRx to evaluate binding affinities (https://github.com/mattroconnor/deep_learning_coronavirus_cure). He identified Remdesivir as a potential COVID-2019 treatment, which Sage Health will be donating to the Wuhan…
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Loading Multiple DLG Files
As you may know, you can use Vina Wizard > Analyze Results page to load multiple Vina outputs (*_out.pdbqt). For AutoDock, if you have already gone through the wizard, produced dlg (docking log) files and want to load them again, you can go through the wizard again to load them. PyRx won’t run AutoDock and will…
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PyRx 0.9.8 Release Announcement
We are pleased to announce the release of PyRx 0.9.8. Major changes in this release include: Added Show Interactions tool in Analyze Results tab for AutoDock and Vina Wizard. Click on the pink icon (highlighted in yellow in the image below) to select receptor and ligand atoms that are in close contacts to each other.…
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HPC and AWS
Please note that this feature requires access to a High-Performance Computing (HPC) cluster. If you already have an HPC cluster setup, which can be very expensive, then you can use the Linux version of PyRx to run on the cluster head node. See, for instance, this link on how Centre for Advanced Computing at Queen’s…
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Recent Changes in Vina Web Services and Mac OS X Updates
There has been recent changes in Vina web services that makes it impossible to run Vina in Remote (Opal Web Services) mode. I’ve uploaded new updates to fix this. Please use PyRx > Help > Check for Updates… menu to apply this update if you are using Linux or PyRx 0.9.7 or higher on Windows.…