Author Affiliation

Math and Science Academy, Ocean Lakes High School

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

DOI

10.25776/zt0x-nv05

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Apr 14th, 12:00 AM Apr 14th, 12:00 AM

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.