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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.

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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.

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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.

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Last Updated on Thursday, 03 September 2009 12:34
Preparing Ligands for Docking PDF Print
Written by Sarkis Dallakian   

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. PyRx also provides options to run energy minimization for selected or all molecules. Energy minimization is done using OpenBabel and we have a GUI that can be used to change energy minimization parameters.

Finally, PyRx has menus for converting selected or all molecules to AutoDock Ligand format (PDBQT). Users have options for removing fragments smaller that specific number (OpenBable.StripSalts) and an option to choose partial charges (OpenBabel or PyBabel from MGLTools).

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Last Updated on Wednesday, 10 February 2010 12:21
Starting Virtual Screening PDF Print
Written by Sarkis Dallakian   

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 Batch Job is that Web Services can be run from Windows or Mac OS X based PC, whereas PBS Batch Job require Unix/Linux cluster. On “Select Ligands” and “Select Macromolecule” page user selects ligands and macromolecule, correspondingly, from the list of available molecules in Navigator pane.

On “Run AutoGrid” page adjust grid box by dragging handles of the VTK box widget before running AutoGrid.


On “Run AutoDock” page user can select among four docking algorithms available in AutoDock 4.0 as well as modify docking parameters used in each algorithm.

“Analyze Results” page is presented at the end of Virtual Screening where binding energies are displayed. Users can sort/filter results or save them as CSV (comma-separated values) for further analysis with third-party spreadsheet programs.. We also provide option for plotting clustering histograms using matplotlib - python 2D plotting library. “Analyze Results” page can also be used to open DLGs (docking log files) from previous AutoDock runs.

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Last Updated on Thursday, 29 September 2011 09:37

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