PyRx – Python Prescription

Virtual Screening Tool

Author: sargis

  • 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…