Publication Date
2022
Conference Title
Modeling, Simulation and Visualization Student Capstone Conference 2022
Conference Track
Education & Training
Document Type
Paper
Abstract
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.
Keywords:
Visualization, Molecular, Chemistry, Biology, Education
Start Date
4-14-2022
End Date
4-14-2022
Recommended Citation
Shen, Ruoming, "A Preliminary Comparative Study of Molecular Visualization Software for Education" (2022). Modeling, Simulation and Visualization Student Capstone Conference. 2. DOI: 10.25776/zt0x-nv05 https://digitalcommons.odu.edu/msvcapstone/2022/education/2
DOI
10.25776/zt0x-nv05
Included in
Biomedical Engineering and Bioengineering Commons, Electrical and Computer Engineering Commons
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.