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PyRx Ligand Docking Tutorial PDF Print
Written by Sarkis Dallakian   

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Last Updated on Saturday, 10 December 2016 19:46
 
2016 Year in Review PDF Print
Written by Sarkis Dallakian   

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!

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Last Updated on Tuesday, 06 December 2016 04:29
 
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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