PyRx – Python Prescription

Virtual Screening Tool

PyRx 1.0 Release Announcement

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We are pleased to announce the release of PyRx 1.0. PyRx is an award winning virtual screening tool used and loved by scientists worldwide. The following are new features included in this release:

  • Added similarity search for the Vina and AutoDock Wizards to find similar compounds in PubChem. You can now right-click on any of the rows under the Analyze Results tab and select Find Similars in PubChem … This searches PubChem using Similarity search, downloads 3D conformers matching search results and opens it with the Open Babel widget.

  • Double click on any of the rows in the Open Babel widget to open PubChem in the web browser matching the Title of the compound. For instance:
    https://pubchem.ncbi.nlm.nih.gov/#query=C20H30O5.

  • On the Vina Analyze Results tab users can now save SMILES strings:

  • For Vina Wizard, on the Run Vina page, when you click on Forward button, PyRx checks to see if there is a Vina output file already present (out.pdbqt) for each ligand. If you have already run Vina, it won’t run a new Vina job again. It instead adds the output to the Analyze Results page. This is useful when you have run Vina for a large number of ligands and would like to add additional ligands without running Vina for every ligand. Users can force PyRx to run Vina for each ligand by pressing Run Vina button.

  • When screening a large number of ligands, you can now limit how many ligands to display in the Analyze Results page for Vina Wizard. This is for computers that don’t have enough memory to load all docking results at once. Use PyRx > Edit > Preferences… and check Limit Docking for GUI Analysis. You can also enter a number of top results to display. PyRx can now sort all results by predicted binding affinity and display only top results in the GUI to avoid running out of memory.
    For screening large libraries of ligands, it is best to use a High-Performance Computing (HPC) cluster with many CPU cores and have PyRx run on a server with large memory (RAM). If you don’t have a server with large memory, this option can be used to limit how many Vina outputs PyRx loads into memory.

The list of changes for all previous PyRx releases is available on our Blog. Please use our ticketing system to report bugs or request new features – https://sourceforge.net/p/pyrx/tickets. We hope you will enjoy this new version of PyRx.