PyRx – Python Prescription

 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.

• Added RMSD from reference structure column to AutoDock Analyze Results table.

• When making flexible residues, PyRx is now using options defined in receptor preparation preferences to decide what type of changes to do.

PyRx 0.9.2, 0.9.3 and 0.9.4 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.4 version is available at PyRx 0.9.4 Release Announcement.

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 shown in the photo below. Have a great holiday season!

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.

New in this release is Edit > Preferences > AutoDock > Receptor Preparation panel as shown in the image below. Users can now keep water molecules when making Macromolecule pdbqt files by unchecking Waters option in the Receptor Preparation Preferences.

PyRx 0.9.3 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.3 version is available at PyRx 0.9.3 Release Announcement.

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 or more Macromolecules.

• It’s now possible to add multiple Macromolecules at once.
• Users can now save docked ligand and macromolecule complex as pdb. Right-click on docked conformation under Analyze Results tab in AutoDock or Vina Wizard to access this option.

• Added Parameter button to Run Vina page to enable users to enter exhaustiveness and num_modes (maximum number of binding modes to generate) parameters for Vina.

• Made Open Babel table sortable.
• Bug fix for making flexible residue to work for larger proteins.
• Added support for Sun Grid Engine (SGE) when running docking jobs on a cluster.

PyRx 0.9, 0.9.1 and 0.9.2 users, please use PyRx > Help > Check for Updates…  menu to update to this version. The list of changes for 0.9.2 version is available at

PyRx 0.9.2 Release Announcement.

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.

Abstract

Virtual molecular screening is used to dock small-molecule libraries to a macromolecule in order to find lead compounds with desired biological function. This in silico method is well known for its application in computer-aided drug design. This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems (Linux, Windows, and Mac OS). Specific steps for using PyRx, as well as considerations for data preparation, docking, and data analysis, are also described.

• PubMed Link http://www.ncbi.nlm.nih.gov/pubmed/25618350

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

We are excited to have new Mac OS X installer available for download. PyRx sells have been good for the past two years, and we thank each and every customer. Your support is much appreciated. Your contributions is what makes it possible to create PyRx installers.

We had 6,299 downloads in 2013 for the free version of PyRx hosted on SourceForge. The table below shows number of downloads broken down by operating system. SourceForge provides excellent tools for download statistics and this table was copied from here. Thank you all for using PyRx.