A Preliminary Comparative Study of Molecular Visualization Software for Education

Chemistry and biology are sciences vital for understanding metabolic processes, developing disease treatments, and improving environmental conditions. With extensive knowledge of biochemistry, we can take advantage of a material’s unique chemical composition and properties in various applications. Visualization software is essential for analyzing complex chemical and biological structures and predicting their interactions with each other. This paper presents a preliminary study of three open source molecular visualization software tools - Visual Molecular Dynamics (VMD), Jmol, and Mol*, and evaluates their strengths and deficiencies. This paper utilizes the March Molecule of the Month, Vascular Endothelial Growth Factor (VEGF), from the Protein Data Bank as a case study. The VEGF is a complex signaling protein that stimulates angiogenesis for building new blood vessels. All three tools handle VEGF well by providing a variety of visualization and analytical capabilities, with Jmol and Mol* better suited for educational purposes and VMD for research purposes. The paper also discusses the author’s interest and intent to contribute to the development of molecular visualization software in the future.