Tools

  • Maestro
    • Molecular Visualization - rotating, zooming, and highlighting specific parts of the molecule
    • Molecular Editing
    • Molecular Docking - a computational technique used to predict how a small molecule (e.g., a drug candidate) interacts with a target protein or receptor. It helps researchers analyze and optimize the binding affinity and orientation of ligands within the target protein’s active site
    • Molecular Dynamics Simulations - simulate the movements and interactions of atoms and molecules over time. This feature helps researchers study the behavior and stability of biomolecules, as well as their interactions with small molecules.
    • Virtual Screening - allowing users to screen large libraries of compounds virtually to identify potential drug candidates
    • Quantitative Structure - Activity Relationship (QSAR) Analysis
  • PyMOL
    • Molecular Visualization
    • Molecular Editing
      • Adding or removing atoms, bonds, and residues, as well as performing basic molecular building tasks
    • Molecular Surface Generation - visualizing the shape and properties of macromolecules. Surface representations can be used to study protein-ligand interactions, protein-protein interactions, and other structural features.
    • Electrostatic Surface Calculation - calculate and display electrostatic potential surfaces of molecules. This feature helps researchers understand the distribution of positive and negative charges on a molecule, which is important for studying molecular interactions.
    • Protein Structure Analysis - analyze protein structures. It allows users to measure distances, angles, and dihedral angles within a protein, as well as perform structural alignments and superpositions.
    • Molecular Dynamics Visualization - read trajectory files generated from molecular dynamics simulations and animate the molecular structures over time, allowing researchers to observe the movements and conformational changes of biomolecules.
    • Scripting and Automation - automate tasks, customize visualization settings, and perform complex analysis workflows. The scripting language used in PyMOL is Python, which provides flexibility and extensibility to the software.
    • Has open source subset: schrodinger/pymol-open-source

Other