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30 Second PyRx Explainer PDF Print
Written by Sarkis Dallakian   

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Last Updated on Tuesday, 10 May 2016 16:19
 
PyRx 0.9.4 Release Announcement PDF Print
Written by Sarkis Dallakian   

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.

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Last Updated on Monday, 04 April 2016 19:30
 
PyRx 0.9.3 Release Announcement PDF Print
Written by Sarkis Dallakian   

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.

  • 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.

vina-parameters

  • 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.

 

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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.

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.

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Last Updated on Sunday, 01 February 2015 11:40
 
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