Home Blog
Pre-Release 0.5 Updates PDF Print
Written by Sarkis Dallakian   

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 dataset from my previous blog post through AutoDock Vina. There are third party packages available for AutoDock Vina such as PaDEL-ADV, VcPpt, MakeVinaCommand and PyMOL plugin. The new version of ADT also has features for working with output files generated by Vina. To explore an option for adding a new Wizard to PyRx for AutoDock Vina, I run AutoDock Vina on our cluster, using a script from Vina Manual. Here are the results:

This is just a proof of concept to show that you can use PyRx to analyse results from different docking programmes.

Add a comment
Last Updated on Thursday, 29 September 2011 09:35
BioAssays and ROC Curves PDF Print
Written by Sarkis Dallakian   

I've got an email from My NCBI about new BioAssay - Limit: Protein 3D Structure. AID: 2158 has Compounds Active: 287Tested: 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 you to plot Binding Energies to provide a bird's-eye view of docking results. In addition, if you have corresponding BioAssay available, you can also plot ROC Curve next to Docking Results. ROC curves appear in many recent publications that prompted me to add this feature to PyRx. Google search on ROC Curve brought me to Receiver operating characteristic - Wikipedia. This page confused me more than it helped me, so I started searching for ROC curve further. I came across Let’s ROC that had the following article mentioned in the comments: Triballeau, N. et al. J Med Chem. 2005, 48, 2534-2547. This article is very well written and it helped me to better understand the use of ROC curves in Virtual Screenings.

This plot shows Docking Results and ROC Curve generated for AID: 2158 BioAssay. Note that results with lowest Binding Energy, as predicted by AutoDock, are active compounds. It might seem that overall AutoDock doesn't do well because some of the points on ROC curve are below the diagonal. However, this all depends on the dataset chosen. If the dataset had only a few active compounds, then chances are, that it would have produced an ideal ROC curve. In that sence, ROC curve, by itself, is not informative, unless you have a plot of Docking Results like the way PyRx does.

Add a comment
Last Updated on Thursday, 29 September 2011 09:34
PubChem BioAssays with Protein 3D Structures PDF Print
Written by Sarkis Dallakian   

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 have been working with qHTS Assay for Promiscuous and Specific Inhibitors of Cruzain (with detergent) (AID: 1478). There were 617 compounds with the 3D records and I selected 1ME4 as a target for docking. After reading corresponding references from PubChem BioAssay and PDB, I prepared input pdbqt files for ligands and macromolecule. Since there were more that 6 ligand atom types, I needed AutoDock version 4.2 or higher. Luckily there is new Autodock4.2.1 service available.To make PyRx aware of this new service, I've added a new page for AutoDock Preferences, where users can change the name of the service, should a new version of AutoDock become available.

I've also made the following changes that will be available in the upcoming release of PyRx:

  • Modified Remote Jobs Query in webSerives; it now updates the GUI after checking each job individually.
  • Made changes to AutoDockPage to make parsing and displaying docking results faster.

You can access the latest version of the code from https://sourceforge.net/projects/pyrx/develop.

As a side note, I was trying to find PubChem Compound ID (CID) for T10. PubChem's Chemical structure search did not recognize InChI provided by PDB. Fortunately, InChI Resolver from ChemSpider was able to read InChI from PDB (ChemSpider ID:  4451401) and I was able to find correpsonding PubChem ID (CID 5289424). It turns out that InChI versions in PDB and PubChem are not the same. It would be nice if there would be a link in Ligand Summary page that PDB displays that would point to a PubChem ID, whenever corresponding ligand is available in PubChem.

Add a comment
Last Updated on Thursday, 29 September 2011 09:36
PyRx Is Now Free and Open Source Software PDF Print
Written by Sarkis Dallakian   

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 PyRx at http://sourceforge.net/projects/pyrx and you are welcome to join the project. Visit https://sourceforge.net/projects/pyrx/develop for more information.

Add a comment
Last Updated on Wednesday, 30 September 2009 13:27
Article in Chemical & Engineering News PDF Print
Written by Sarkis Dallakian   

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:

Also, I'll be presenting PyRx during Virtual Screening & Computer Aided Drug Design training session at the Summer Institute organized by National Biomedical Computation Resource (NBCR). Here is a link to the outline titled Getting Started with PyRx.

Add a comment
Last Updated on Thursday, 03 September 2009 12:34

Page 7 of 8
Get PyRx