Here is a listing, with download links where applicable, of computer software that is useful for the visualization of biomolecules. Software packages listed on this page are not commercially endorsed by either myself or Tennessee Technological University, and I am not receiving any form of compensation for listing them here. This list serves the purpose of providing users with easily-accessible links to download the packages that are used by the tutorials featured on this site.
Click on the link in the heading below of each online software package to access the website.
Avogadro
Avogadro is free molecular modeling software for visualizing and editing small molecules. While it can technically handle large biomolecules and proteins, I do not recommend it for such molecules, as it is not designed for them and there are superior modeling software packages available. This would be the ideal software package to use for quickly building and optimizing a ligand or drug candidate for docking calculations.
Chimera X
Chimera X is a molecular visualization program available from the Resource for Biocomputing, Visualization and Informatics at the University of California at San Francisco. It is free for academic, government, non-profit or personal use. This package provides publication-quality graphics and excellent visualization capabilities in an easy-to-use interface for even novice users. It also provides an interface to Google Colab and Alphafold2 for predicting the 3D structure of protein complexes.
MOE 2024
The Molecular Operating Environment (MOE) available from Chemical Computing Group, Ltd., is a full-featured molecular modeling software package that has a wide variety of applications and features. It is commercial software, so it is not free, although academic pricing is available, and the company has special deals for educators and classroom use. Similar to Chimera X, MOE provides publication-quality 3D molecular visualization, as well as structure-based and ligand-based drug discovery tools, antibody and biologics design, virtual screening, structural bioinformatics, and interface to Gaussian ’09 (quantum mechanics), an interface to NAMD (molecular dynamics simulation), cheminformatics and QSAR tools, and a host of other features.
VMD: Visual Molecular Dynamics
VMD is a 3D biomolecular visualization package for displaying and animating large biomolecular proteins. It was designed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign as a visualization tool for output from the NAMD (Scalable Molecular Dynamics) software. So, in a sense, this is actually 4D biomolecular visualization software. The interface is easy-to-use, although not quite as intuitive as Chimera X and MOE 2024, so this would not be software that I would recommend to students beginning their study of proteins and biomolecules. Yet it is excellent, and award-winning, software and widely used among scientists in biophysical chemistry.