BioGem Blog

Intermolecular interactions are weak bonds formed due to electron sharing between two or more atoms to hold a molecule together. In molecular modelling or computer-aided drug designing (CADD), intermolecular interaction studies are performed to analyze the stability/energy of docking molecules. This video tutorial demonstrates two-dimensional (2D) plot and three-dimensional (3D) molecular visualization of protein-ligand and protein-protein inter-molecular interactions using LigPlot + /LigPlus tool. LigPlot + is a successor of original LigPlot program. The protein-ligand inter-molecular interactions are computed using LigPlot program and protein-protein or domain-domain inter-molecular interactions using DimPlot program. Moreover, the interactive 3D molecular visualization of the computed result can be viewed using RasMol or PyMOL. List of softwares used in this tutorial are LigPlot + , LigPlus , RasMol , PyMOL , and JDK .

Introduction to PyMOL PyMOL is a Python-enhanced OpenGL based molecular visualization tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is available at SourceForge.net ( https://sourceforge.net/projects/pymol/ ) for free to everyone. The commercial graphical end PyMOL is developed, maintained and distributed by Schrödinger, Inc ( https://www.pymol.org/ ). PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. Requirements for PyMOL Installation In this tutorial, I have explained how to install the latest PyMOL software (the latest version of PyMOL software as on September 15, 2016 is 1.8.3.2) for free. I have chosed Windows 10 Enterprise OEM 64-bi...