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…

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…

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.…

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…