PyRx – Python Prescription

We are looking for a co-founder to work on PyRx. Someone who knows Python and computational chemistry and can contribute to this project. If you are interested, please email your Resume to dallakyans@gmail.com. The screenshot below is from zoominfo. The numbers are not accurate, but nice to have.

We are pleased to announce the release of PyRx 0.9.9. This is the first release since COVID-19 pandemic. This pandemic showed how important open science is for fighting emerging diseases. Since the earlier days PyRx has been actively used to find treatment for COVID-19 and there has been numerous publications using PyRx to find potential drug candidates against COVID-19. Our free version passed 113k downloads worldwide. A screenshot below shows geographic distribution of these downloads with darker green counties having the most downloads (India, United States and China are in the top 3).

Here are the main changes for PyRx 0.9.9 release:

• In Analyze Results tab for AutoDock and Vina Wizard you can now delete multiple selected entries at once using Delete icon on the upper right corner. You can also save multiple selected entries as SDF file with right mouse click. Thanks to Prof. Cheol-Min Park for requesting this feature.

• In Open Babel widget, you can now open multiple molecules at once.
• Fixed slow exit on Windows.
• Removed Remote (Opal Web Services) execution mode since NBCR and its associated websites/services have been retired as of April 30, 2020.

The list of changes for all previous PyRx releases is available on our Blog. Check out also our Facebook page where we post latest video tutorials and links to PyRx related publications.

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.

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. Unfortunately PyRx update procedure doesn’t work on Mac OS X or on Windows with PyRx 0.9.6 and earlier versions. Please use the following steps to update PyRx instead.

Step 1, visit https://sourceforge.net/p/pyrx/code/HEAD/tree/PyRxDev/ and click on Download Snapshot.

Step 2, uncompress this downloaded file and locate PyRxDev/PyRx folder.

Step 3, make a backup copy of the following folder, by renaming it to PyRx.bak for instance, in case PyRx fails to start after this update:

• Windows PyRx 0.9.6 or earlier – C:\Program Files (x86)\PyRx\$Version\Lib\site-packages\PyRx
• Windows PyRx 0.9.7 or older – C:\Program Files\PyRx\$Version\Lib\site-packages\PyRx
• Mac OS X – /Library/PyRx/$Version/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx

$Version here is the version number of PyRx (e.g. 0.9.6)

Step 4, replace this folder with the one you downloaded above.

If you have updated PyRx previously using Help > Check for Updates… menu, delete .PyRx_workspace\update from your home directory.

Please let me know if you have questions or need more information.

We are pleased to announce the release of PyRx 0.9.7. We have upgraded Python interpreter on Windows to 64 bit version that allows users to work with larger molecules. Other major changes in this release include:

For Inverse Virtual Screening with Vina, we now have preferences page where users can specify maximum number of Macromolecules to load.

Added Lipinski Rule of Fives in Open Babel table filter.

Open Bable table now includes logP, number of hydrogen bond donors (#HBD) and acceptors (#HBA) columns.

Implemented Max Runtime in PyRx > Edit > Preferences. Users can change this to terminate all local jobs that take more than Max Runtime (in minutes) to run.

PyRx 0.9.6 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.6 version is available at PyRx 0.9.6 Release Announcement.

We are pleased to announce the release of PyRx 0.9.6. Major changes in this release include:

When making pdbqt for Macromolecules that have atoms at alternate locations, users can now generate all possible combinations.

Individual residues can now be displayed as Balls and Sticks.

A new option to choose Formula_Title for the name of the ligands when making AutoDock Ligand pdqt files using Open Babel widget. Use PyRx > Edit > Preferences, click on + icon next to Open Babel and select AutoDock Ligand. You’ll see a new option there next to “Name Converted Ligand Using”. There are two options: Title or Formula_Title. If you select Formula_Title, next time when PyRx makes AutoDock ligands using Open Bable, it will name ligands accordingly.

Option to toggle on and off balloon widget shown below.

PyRx 0.9.5 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.5 version is available at PyRx 0.9.5 Release Announcement.