Protein-Ligand Binding Site Analysis using Chimera

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. This is a video tutorial for prediction of protein-ligand atom interactions and Ramachandran plot using Chimera tool. In this tutorial, I have used a Ascaris hemoglobin domain protein structure retrieved from the Protein Data Bank (PDB ID: 3C33).

Note: In Chimera, atoms/molecules are selected by three methods: (i) Ctrl+Left-click for one atom section, (ii) Ctrl+Shift+Left-click for two atoms section, and (iii) Ctrl+Left-click+Up Arrow for whole molecule section.