PyRx – Python Prescription

Virtual Screening Tool

Author: sargis

  • Known Issues and Feature Requests

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    An incomplete download is the most common reason for non working installers. Make sure your download is complete before running installers. “Customize Filter” widget for table editor causes crash on Mac. PyRx crashes on Linux when there are no hardware 3D accelerated (OpenGL) drivers avialable. See Using hardware accelerated 3D renderer on Linux and Installing…

  • Article in Chemical & Engineering News

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    I’m happy to announce that PyRx has made into Chemical & Engineering News. Please refer to the following publication if you’d like to cite PyRx in your article: L.K. Wolf, C&EN 87, 31 (2009) Also, I’ll be presenting PyRx during Virtual Screening & Computer Aided Drug Design training session at the Summer Institute organized by…

  • Molecular Surface and Mayavi

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    Molecular Surfaces Using IsoSurfaces Mayavi User Guide

  • Tables Widget and New Features in PyRx 0.5

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    Blog post mentioned in the video:Thermal Shift Assay for Inhibitors of 15-Hydroxyprostaglandin Dehydrogenase

  • Getting Started Screencasts

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    Shows how to prepare ligand and use AutoDock Wizard. Please note that pdb structure has been changed since I made this video (see, for instance, pdb-l: Modifying existing PDBs and pdb-l: Chain order changes: a problem for Proteopedia). Please use PyRx’s built-in text editor available under Documents tab (or any other text editor) as described…

  • List of Changes in PyRx Version 0.5 and Earlier

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    The following are list of changes in PyRx version 0.5 and earlier: Version 0.5 – 25 March 2010 Added Save as Comma-Separated Values (CSV) tool for database tables. Added plotting feature for database tables. This feature can be accessed through a toolbar button under Tables tab. By default, it opens up Table Plotting Dialog where…

  • Preparing Ligands for Docking

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    Molecular Libraries that are available from PubChem or elsewhere, usually contain 2D structures generated from molecular formulas or SMILES strings. To prepare these files for docking, PyRx is using OpenBabel to parse Structured Data Format (SDF). TableEditor from enthought.traits allows users to sort/filter molecules. The results are displayed in TVTK scene as sticks and balls.…

  • Starting Virtual Screening

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    When all input structures are ready for docking, start Virtual Screening by using AutoDock Wizard widget shown below.     On the first page select whether to run AutoDock locally or remotely (buzzword: cloud computing) using Opal Web Services Toolkit developed at National Biomedical Computation Resource (http://nbcr.net). The advantage of using Web Services over PBS…