PyRx - Virtual Screening Tool News

We are pleased to announce the release of PyRx 1.1. The following are new
features included in this release:

• Machine Learning Scoring Function: Integrate the powerful RF-Score V2 machine learning scoring function to accurately assess docked poses or imported
• ADME Radar Chart: Create customizable radar charts that depict ADME-related properties for OpenBabel molecules, offering a holistic view of their molecules binding affinity.
• 2D-Structure Visualization: Explore the 2D-structure of the OpenBabel molecules along with a list of the associated properties and pharmacokinetic profiles
• Quick Filter: Simplify data analysis with easy-to-use min/max filtering options for docking results or OpenBabel molecules.
• Interactive Plotting: Customizable and interactive scatter plot and histogram for OpenBabel molecules
• Automatic Grid Box Centering: Optimize docking grid box positioning effortlessly by centering on a specific residue of the receptor. Enhance precision in molecular docking studies.
• Ramachandran Plot: Assess protein structure with an interactive and customizable Ramachandran plot. Gain valuable insights into the conformational quality of protein residues.
• Protein Structure Insights: Perform analyses on protein structure, including residue-type distribution, heteroatoms exploration, and more.... read more

We are pleased to announce the release of Dockamon - PyRx 1.0. This is a work
in collaboration with
CrescentSilico.
Dockamon - PyRx is a structure-based drug design software package containing
two integrated software programs: Dockamon and PyRx. Dockamon is software for
scoring ligand docked poses using machine learning scoring functions. PyRx is
molecular docking and virtual screening software. Major features of Dockamon
include:... read more

We are pleased to announce the release of PyRx 1.0. PyRx is an award winning
virtual screening tool used and loved by scientists worldwide. The following
are new features included in this release:

• Added similarity search for the Vina and AutoDock Wizards to find similar compounds in PubChem. You can now right-click on any of the rows under the Analyze Results tab and select Find Similars in PubChem ... This searches PubChem using Similarity search, downloads 3D conformers matching search results and opens it with the Open Babel widget.
  ... read more

PyRx has been recognized with the following awards by SourceForge:

Community Leader
Community Choice
Open Source Excellence
SourceForge Favorite

Community Choice

SourceForge Favorite

Community Leader

Open Source Excellence

These honors are awarded only to select projects that have reached significant
milestones in terms of downloads and user engagement from the SourceForge
community. This is a big achievement, as PyRx has qualified for these awards
out of over 500,000 open source projects on SourceForge.... read more

PyRx has been recognized with the following awards by SourceForge:

Community Leader
Community Choice
Open Source Excellence
SourceForge Favorite

Community Choice

SourceForge Favorite

Community Leader

Open Source Excellence

These honors are awarded only to select projects that have reached significant
milestones in terms of downloads and user engagement from the SourceForge
community. This is a big achievement, as PyRx has qualified for these awards
out of over 500,000 open source projects on SourceForge.... read more

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.

link

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).... read more

link

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.... read more

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. He identified Remdesivir
as a potential COVID-2019 treatment, which Sage Health will be donating to the
Wuhan institute of Virology for further analysis.... read more

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.... read more

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.... read more

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 Windows or Linux. Unfortunately PyRx update procedure doesn't work on Mac OS X. Please use the following steps to update PyRx on Mac OS X.... read more

link

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.

... read more

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.

... read more

We are pleased to announce the release of PyRx 0.9.5. Major changes in this release include:

• Fixed a bug when toggling hydrogen bonds using toolbar icon.
• PyRx can now run docking for molecules that have quotes in their names, like in 3-hydroxy-5_7_3'_4'_5'-pentamethoxyflavone.
• Added balloon widget to draw labels when the mouse stays above a molecule. This can be helpful when there are multiple molecules in 3D scene. The mouse cursors changes to busy when you move the mouse over a molecule. You can disable this by deleting a single line - https://sourceforge.net/p/pyrx/code/278/tree/PyRxDev/PyRx/mayaviEngine.py#l110 . Let me know if you don't like this feature; I can add an option to disable this in the next release of PyRx, if needed.... read more

link

2016 has been a great year for PyRx. We have passed 35k downloads, which is excellent for a scientific software . There have been many new publications mentioning PyRx; it's nice seeing PyRx used for research ranging from Anticancer to Zika. PyRx now has a Facebook page and we also run Facebook and Googe AdWords advertising. The best news for 2016 is that we moved to our new headquarters with a beautiful view of Bonita Golf course show in a photo below. Have a great holiday season!... read more

link

We are pleased to announce the release of PyRx 0.9.4. In this release we fixed a bug introduced in 0.9.3 that would not properly update search space dimensions. We are also now offering a bug bounty for all original bug reports that are not listed under Known Issues. The exact amount for bug bounty depends on the severity of the bug and the percentage of impacted users.... read more

We are pleased to announce the release of PyRx 0.9.3. This version includes minor fixes as well as all the features/fixes listed below:

• Implemented Inverse Virtual Screening for AutoDock and Vina. What this mean is that users can now select multiple Macromolecules as well as multiple Ligands and PyRx would run the docking of one or more Ligands against one ore more Macromolecules.

... read more

link

I'm excited to have a book chapter on PyRx published in a book from Springer Publishing titled “Chemical Biology – Methods and Protocols”. I'm very thankful to editors for the opportunity to publish this work and they did a great job in compiling and editing this book. See the Table of Contents that includes many interesting methods and protocols used in modern Chemical Biology. In particular, Small-Molecule Library Screening by Docking with PyRx describes utilization of this essential software tool for the field of chemical biology and highlights key considerations and strategies for performing molecular docking.... read more

This is a brief introduction to PyRx workspace. It shows where PyRx stores different files and how to create a new workspace.
link