PyRx – Python Prescription

Virtual Screening Tool

PyRx 1.2 Release Announcement

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by

sargis
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We are pleased to announce the release of PyRx 1.2. The following are new features included in this release:

  • Fix for AttributeError in PyRx: “vtkAssembly object has no attribute ‘tuber’. This would happen when the number of atoms on ligand is > 200.
  • Automatic Binding Site Detection: a method for automatically detecting possible binding sites in a given macromolecule (Analysis->Detect Binding Sites). Automatic binding site detection is useful for docking in cases where the binding site is not known. The method is from the DeepChem package, which is considered useful for preliminary detection of binding sites in a protein structure. Is it based on the convex hull method:
    Saberi Fathi SM, Tuszynski JA. A simple method for finding a protein’s ligand-binding pockets. BMC Struct Biol. 2014 Jul 19;14:18. doi: 10.1186/1472-6807-14-18. PMID: 25038637; PMCID: PMC4112621.
  • Binding Sites Panel: a panel for managing binding sites (i.e. docking grid boxes) and for displaying the detected binding sites, visualization in 3D, manual creation, importing/exporting, etc. the When binding sites are detected using the detect binding sites feature mentioned, the binding sites are added to the list of this panel. When a binding site is selected, it will be displayed in the 3D-Viewer; the opacity can be adjusted via the slider. It is also possible to manually create a binding site and add it to the list via the create button. The binding sites can be exported/imported as well.
    In the Vina wizard, when setting the grid box position/size, the user can select a per-detected/created binding site directly as the docking grid box via the From Binding Site … button.
  • Charge Distribution Visualization: When a ligand is selected from the OpenBabel table, the charge distribution of the atoms is displayed in a new tab in the Structure Details Panel named Charge Distribution.
  • AlphaFold Database structures fetching: This new feature is available via File->AlphaFold Database… menu. Users can download the structure either by UniProt ID or AlphaFold ID. For example: UniProt IDs: P00734, P02768. AlphaFold IDs: AF-Q16539-F1, AF-P04637-F1.