PyRx – Python Prescription

Virtual Screening Tool

Author: sargis

  • ParaDockS

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    There is a new article in J. Chem. Inf. Model. that talks about ParaDockS. This is the only other docking program, besides AutoDock 4 and Vina, that is open source. Congradulations to ParaDockS team for making such a great product available! This means that PyRx can some day use ParaDockS and vise versa, so here…

  • Frequently Asked Questions

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    Is there a user’s manual for PyRx? How to report a bug. How do I cite PyRx. How to sort the table in Analyze Results tab. How to reset perspective and restore the default PyRx arrangement? Keyboard and mouse interaction with 3D Scene. How to clean your PyRx workspace. Docking instance has no attribute ‘ligMol’.…

  • Thermal Shift Assay for Inhibitors of 15-Hydroxyprostaglandin Dehydrogenase

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    Here are the results of a new PubChem BioAssay AID: 2427 with 42 compounds (22 active, 2 inactive and 18 inconclusive). AutoDock did a perfect job here giving favourable binding energy for active compounds compared to inactives. As a result, we have a prefect ROC curve here. I made the makers bigger so you can see…

  • qHTS Assay for Inhibitors of Dna Helicase

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    I’ve got another email from My NCBI (Subject: What’s new for ‘BioAssay – Limits: Protein 3D Structure). It was about AID: 2353 – qHTS Assay for Inhibitors of RecQ-Like Dna Helicase 1 with 23 active and 1272 tested compounds. There are 2 Links for Protein Structure corresponding to open and closed conformations. I run virtual…

  • Open Babel Partial Charges

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    When preparing ligands for docking PyRx users can select between PyBabel (MGLTools) and Open Bable partial charges using Edit -> Preferences menu. See PyRx Screencast – Open Bable for details. PyRx is using PyBabel charges, by default. I run the dataset from my previous blog post, using Open Bable, to see if I can get…

  • Pre-Release 0.5 Updates

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    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…

  • Neuraminidase, Sialic Acid, Relenza and Sugar

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    Neuraminidase, Sialic Acid, Relenza and Sugar from Sarkis Dallakian on Vimeo. Watch this video in HD on Vimeo. Links used in the screencast – Relenza, Neuraminidase, Sugar and ws.nbcr.net.  

  • BioAssays and ROC Curves

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    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…

  • PubChem BioAssays with Protein 3D Structures

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    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,…

  • PyRx Is Now Free and Open Source Software

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    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…