I’ve added instructions on how to update to the latest version from Source Code and how to submit a feature equest to Downloads page. The major new feature in 0.5 is database table plotting feature that can be used for BioAssays and ROC Curves. To compare ROC curves generated by two different docking algorithms, I run the…

I’ve got an email from My NCBI about new BioAssay – Limit: Protein 3D Structure. AID: 2158 has Compounds Active: 287; Tested: 572; it’s exaclty that I was looking for. Based on this data, I’ve implemented new features that will available in upcoming 0.5 release. Interested users can check it out right away. The new feature allows…

I started searching PubChem BioAssays and limited results to the ones that link to Protein 3D Structure. There are currently only 61 BioAssays available. I wanted to select a BioAssay that would have around 100 compounds tested, but only handful that are active. In order to test PyRx and see what new features to add,…

I’ve got a green light from our Office of Technology Development to distribute PyRx under Open Source BSD License. For users, this means that you are free to use PyRx for academic as well as commercial purposes. For potential developers, this means that you can now contribute code to PyRx. I’ve created a project for…

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…