BioGem Blog

Chimera (or UCSF Chimera ) is an interactive molecular visualization and analysis program developed by the Resource for Biocomputing, Visualization, and Informatics ( RBVI ) at the University of California, San Francisco ( UCSF ). ChimeraX (or UCSF ChimeraX ) is the next-generation molecular visualization program, which is a successor of Chimera. The Chimera/ChimeraX program supports analyzing various molecular structures and related data, including sequence alignments, docking results, molecular assemblies, electron density maps, trajectories, and conformational ensembles. It can be downloaded freely for academic, government, nonprofit, and personal use. Protein-Ligand Interaction Models In the protein-ligand interaction model, proteins or ligands are represented by a wire-frame model / stick model / ball-and-stick model / cartoon model / space-fill model / surface model, but not both. The interactions between protein and ligand atoms is represented by dotted or dashed lines. T...

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 .