Home Blog PubChem BioAssays with Protein 3D Structures
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.

blog comments powered by Disqus
Last Updated on Thursday, 29 September 2011 09:36
Get PyRx