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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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