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 be a better alternative.There are a number of publications using PyRx to find new drugs for Covid-19 treatment. Given the time it takes for a toxicity study of a novel drug, repurposing existing drugs seems a more feasible option.

The number of downloads has increased during the pandemic. There have been around 20k downloads year to date (9/5/2020) compared to 10k downloads for the same period last year. This pandemic also emphasized that PyRx can live long after I'm gone, which is a good thing.

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 institute of Virology for further analysis.

Happy to see that the free version is still working on Windows (since 2011), unlike Mac version, that gives me nothing but headaches. We do not plan to increase the price of PyRx anytime soon and hope that our website and the store will remain online during these troublesome times.

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 load the results instead, if all dlg files are in their places. PyRx stores dlg files in subfolders and since a file browser won't let you select multiple files from different folders, it's not currently possible to load dlg files using a file browser.

I've created a new script to enable this. Download load_dlgs.py and use PyRx > File > Run Python Script or click on Python icon on the toolbar on upper left to open this file. It opens Choose Docking Log Files dialog where you can select multiple dlg files. Please note that some of the PyRx functions, such as recently introduced Show Interactions, won't work and will through error messages if you load dlg files this way.

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. It also shows hydogen bonds as green lines if there are any hydrogen bonding interactions.



• Added a new tool in the toolbar for selecting residues inside a sphere. By default, it will place the center of the sphere at a center of the current selection, or if nothing is selected, it will place the center at the center of the first molecule in the 3D scene.

  

  The center and radius of the sphere can be changed by clicking on a sphere and zooming or panning. To enter numerical values for center and radius use Navigator > TVTK, expand the tree and double-click on SphereRepresentation.

  

• You can now run Vina jobs on Amazon Web Services and pay as you go for the resources used.

  

  Read HPC and AWS article to learn how to use this.