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How to Filter Tables in PyRx PDF Print
Written by Sarkis Dallakian   

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Last Updated on Saturday, 20 June 2015 21:27
Book Chapter on PyRx in Chemical Biology - Methods and Protocols PDF Print
Written by Sarkis Dallakian   

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.


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.

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Last Updated on Sunday, 01 February 2015 11:40
Introduction to PyRx Wrokspace PDF Print
Written by Sarkis Dallakian   

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

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New Mac Installers Are Available for Downloads PDF Print
Written by Sarkis Dallakian   

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.

Operating System Downloads
Windows 4,050
Linux 1,458
Macintosh 641
Unknown 144
Android 6
Total 6,299
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Last Updated on Sunday, 22 November 2015 11:56
PyRx 0.9.2 Release Announcement PDF Print
Written by Sarkis Dallakian   

We are pleased to announce the release of PyRx 0.9.2. One of the main new feature implemented in PyRx 0.9.2 is an option to execute AutoDock 4 or Vina using remote execution mode as shown in the image below. This is a great feature for users who want to run docking on a remote cluster without using CPU cycles of their Desktops.

PyRx 0.9 and 0.9.1 users, please use PyRx > Help > Check for Updates...  menu to update to this version. The following are new features and bug fixes implemented in 0.9.2 release:

[r216] Resource/Workspace Folder is now at user.home + os.sep + '.PyRx_workspace'.
[r196] Enabled AutoDock remote execution mode thanks Autodock 4.2.3 web service running at http://nbcr-222.ucsd.edu/opal2.
[r194] Enabled Vina remote execution mode thanks Vina 1.1.2 web service running at http://nbcr-222.ucsd.edu/opal2.
[r191] Removed Radicals using SetSpinMultiplicity(0) in ConvertToOB. Otherwise sdf files created by PyRx had "M RAD..." line and we couldn't read these sdf files back into PyRx. Thanks to Scott A Reiling for reporting this bug.
[r188] Set stereo=True on for Windows only. Otherwise it crashes on Linux.
[r187] Changed Macromolecule names to lower case to handle Windows' case insensitive file systems.
[r185] Help -> About dialog now shows update date, if applicable.
[r183] Fixed an issue when opening Vina output files via File -> "Load Molecule" menu.
[r176] Added '--out' option for Vina to save output files in the Macromolecules folder.
[r175] Fixed an issue with ligand_types for flexible residues.
[r174] When selecting a macromolecule, ignore "*_out.pdqt" files to insure proper selection.
[r173] Made navigation between different tabs in AutoDock Wizard more stable.

See also: PyRx 0.9.1 Release Announcement.

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Last Updated on Monday, 26 May 2014 10:13

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