We are pleased to announce the release of PyRx 1.1. The following are new features included in this release:
- Machine Learning Scoring Function: Integrate the powerful RF-Score V2 machine learning scoring function to accurately assess docked poses or imported
- ADME Radar Chart: Create customizable radar charts that depict ADME-related properties for OpenBabel molecules, offering a holistic view of their molecules binding affinity.
- 2D-Structure Visualization: Explore the 2D-structure of the OpenBabel molecules along with a list of the associated properties and pharmacokinetic profiles
- Quick Filter: Simplify data analysis with easy-to-use min/max filtering options for docking results or OpenBabel molecules.
- Interactive Plotting: Customizable and interactive scatter plot and histogram for OpenBabel molecules
- Automatic Grid Box Centering: Optimize docking grid box positioning effortlessly by centering on a specific residue of the receptor. Enhance precision in molecular docking studies.
- Ramachandran Plot: Assess protein structure with an interactive and customizable Ramachandran plot. Gain valuable insights into the conformational quality of protein residues.
- Protein Structure Insights: Perform analyses on protein structure, including residue-type distribution, heteroatoms exploration, and more.
Features Details:
* Machine Learning Scoring Function: PyRx offers scoring of ligands using the RF-Score V2 scoring function, which is a machine learning scoring function with signficantly higher binding affinity prediction accuracy compared to the classical AutoDock and AutoDock Vina scoring functions. You can score docked poses from the results of AutoDock/AutoDock Vina docking process or ligands imported in the OpenBabel table. To score ligands (i.e. estimate binding affinity) towards a macromolecule using the RF-Score V2 scoring function, from the Scoring Menu, click Score Ligands, the score ligands dialogue will be opened.
Select the macromolecule (you can choose from molecules in Molecules Navigator) and the table of ligands to score. You can exclude heteroatoms from the macromolecule in the scoring process by checking the Exclude heteroatoms from macromolecule, which can be useful to exclude ligand and solvent atoms if present. The path to the “rf-score-vs.exe” executable should be also specified. After clicking Ok, the ligands will be scored and the result will be added as a column to the corresponding table. The values are the pK (the -log of the activity) calculated by the RF-Score V2 scoring function. Higher values indicate higher estimated activity.
* When selecting a molecule in the Open Babel widget, you can now see the 2D structure of the molecule.
Click the Details tab for the radar chart showing Molecular Weight, number of hydrogen bond donors (HBD), number of rotatable bonds (#Rots), octanol-water partition coefficient (LogP), and the number of hydrogen bond acceptors (HBA) in blue. The light green area shows where these values satisfy the Lipinski Rule of Five. You can also click on HBDs or HBAs checkboxes to highlight in Open Babel 3D viewer hydrogen bond donors in red and hydrogen bond acceptors in blue.
* Quick Filter: To filter the molecules table, click on the Quick Filter icon in the desired table (OpenBabel Tab or Autodock/Autodock Vina Analyze Results Tab). The Quick Filter dialogue shows the columns available for filtering. For each column you can check the Enable checkbox to include the column in the filtering process. Use the min/max sliders to determine the desired range of values. The min/max values are inclusive and the enabled filters are applied using AND operator. The results are applied directly on the table. When closing the Quick Filter dialogue, the table will be reset.
* Interactive Plotting: Click on the 2D-Plots tab to show scatter/histogram plots. Select the axes columns (X/Y for scatter plot, X for histogram) and the values of the OpenBabel molecules will be plotted. Click on the settings icon to customize the plot options such as marker color, size, etc. In the scatter plot, you can click on a point to select the corresponding molecule.
* Automatic Grid Centering: When setting up the grid box for docking (AutoGrid/Autodock Vina), you can center the grid on a residue of the selected macromolecule for the docking process. Click on the “Center on Residue” button, then select the desired residue and click OK, the grid box center will be set to the coordinates of the selected residue.
* Ramachandran Plot: To generate a Ramachandran plot for a protein molecule, from the Analysis menu, click Ramachandran Plot, then select the desired macromolecule (you can choose from molecules in Molecules Navigator). The Ramachandran plot will be generated for the selected protein. You can view the plot in the Ramachandran Plot tab. Each point represent a residue, you can click on a point to display the residue name and angles values.
* Protein Structure Insights: You view a report of a protein structure details, from the Analysis menu, click Protein Structure Details, then select the desired macromolecule (you can choose from molecules in Molecules Navigator). A result of the analysis will be displayed containing general information about the protein structure. Also, chain information, standard residue distribution, heteroatoms residues and water residues information will be displayed.
