Welcome to 3D Biochemistry at Tennessee Technological University! The purpose of this site is to provide a teaching resource and molecular modeling and visualization tutorials for students learning biochemistry. Perhaps one of the most important — and arguably, the most difficult — aspect of studying biochemistry is learning and realizing that biomolecules are in 3D. Polymerized molecules, such as proteins and nucleic acids, are also very large molecules with thousands of atoms. Did you know that one human DNA molecule is approximately the length of your fingernail?
The challenge when visualizing and working with such large, three-dimensional molecules is visualizing them on a two-dimensional computer screen, as well as determining which parts of the molecule are important in your visualization, to highlight those parts while hiding less important parts. This makes the process of visualizing biomolecules almost as much of an art as it is a science. As this site is developed, I hope to demonstrate to students, as well as other faculty, how to use a variety of 3D visualization software through a series of interactive lessons and video tutorials. While I will be recommending several specific software packages, my recommendation is an academic recommendation based on a variety of factors, such as the availability of an inexpensive academic version for educators and students as well as ease of use. I am not recommending software based on a commercial endorsement nor am I or Tennessee Technological University receiving any funds for the recommendation.
About The Author
Dr. Derek Cashman (Dr. Cash) currently serves as a Lecturer in the Department of Chemistry at Tennessee Tech. He has taught biochemistry and physical chemistry courses in the department since 2013. Prior to that, he was a Research Associate at the Center for Molecular Biophysics at Oak Ridge National Laboratory and the University of Tennessee at Knoxville studying photosystem I and bacterial chemotaxis. He completed postdoctoral research in the Department of Chemistry & Biochemistry at Northern Arizona University and the Department of Computational & Systems Biology at the University of Pittsburgh, studying the computational chemistry of small molecule/nucleic acid interactions and protein dynamics. Originally hailing from Chicago, Illinois, he is an avid fan of Chicagoland sports teams, including Da Bears, Da Bulls, Da Cubs, and Da Blackhawks!
About the Masthead Image
The image appearing on the main page of this site depicts the 3D structure of glucose and inorganic phosphate (space-filling representation) in the active site of recombinant human hexokinase. The PDB coordinates were downloaded from the RCSB Protein Data Bank using the accession code 1HKC using the MOE 2024 software, commercially available from Chemical Computing Group, Ltd., Montreal, Quebec, Canada.
