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Protien Modeling Event
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What's New From the CBM?

A New Antibody MAPS Module

Posted 1-6-2021

This new MAPS Module will focus on antibodies and their role in our immune system. With everyone’s current focus on a coronavirus vaccine, we thought this would be a timely topic. There are many fascinating stories of current research involving antibodies that your students can explore.

An obvious choice would be the structure of an antibody binding to a coronavirus protein. We will highlight one fascinating story involving a synthetic biology approach to create a nanobody (single-domain antibody) that locks down the coronavirus spike protein into an inactive conformation.

This paper describes our work over the past twenty years. Check it out, and see how you relate to various aspects of our program!

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Check out the Molecule Maker!

Posted 1-6-2021

Many schools now have access to low cost 3D printers, but finding 3D print files (.STL) of specific small molecules can be challenging.

With the CBM's new Molecule Maker, students and teachers can draw chemical structures and export their molecule as an .STL file for 3D printing. The left side of the screen is an interactive chemical draw program called JSME Molecular Editor. This chemical draw program communicates with the live Jmol program on the right side of the screen, displaying the molecule in a fully interactive 3-dimensional display.

Any small molecule created with the CBM's Molecule Maker can then be exported as an image (.JPG), a molecular structure file (.MOL) or a 3D print file (.STL) that can be used on any desktop 3D printer. Check it out at

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A New CBM Publication

Posted 1-6-2021

The CBM has just published a paper in the Journal of STEM Outreach entitled "A Strategy for Sustained Outreach in the Molecular Biosciences".

This paper describes our work over the past twenty years. Check it out, and see how you relate to various aspects of our program!

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What are Physical Models?

The invisible world of molecules becomes real when students hold physical models in their hands. Models function as thinking tools that stimulate questions and are a key component of the Next Generation Science Standards.

The MSOE Center for BioMolecular Modeling uses 3D Printing Technology to create physical models of protein and molecular structures. They are designed using the molecular Visualization software Jmol and then exported as 3D files.

What Teachers and Students are Saying About the CBM

"Models give the students an opportunity to discover on their own, rather than having you tell it to them."

"These curriculum modules tie what seems like a really abstract idea--some little change in a molecule you can’t even see—to their own health. That’s really compelling. This stuff isn’t in any textbook."

"The fact that they were so teacher-focused was refreshing."

"The CBM staff let us be learners, and they respected us."

"Watching the CBM staff, who are masters, and being given these models is wonderful. Now we have powerful knowledge and powerful examples that we can put in our kids’ heads. I’m so excited for the school year to start, I don’t want to have to wait two months!"

"It was an amazing workshop. Foundational pieces of biology are woven through these stories."

"It really opened up science to me as a student. Science isn't sitting in a classroom learning about rocks its about being in a lab doing research alongside your mentor."

The [MAPS] Team program has taught me the importance of actively participating in the scientific community, being professional, and having the ability to take something complex and put it into simpler yet accurate terms."

"This program has opened my eyes to an entirely new career field. I have learned so much through this experience and I am extremely grateful that I have experienced this."

Selected Publications

Baeten, J., Munzenmaier, D., Vogt, G., Hoelzer, M. and Herman, T (2020) A Strategy for Sustained Outreach in the Molecular Biosciences. J. STEM Outreach Vol 3, Issue 3

Goodsell, D., Franzen, M. and Herman, T. (2018) From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives. J. Mol. Biol. 430(21): 3954-3968

Harris, Michelle A., Peck, Ronald E., Colton, Shannon, Morris, Jennifer, Neto, Elias Chaibub and Kallio, Julie. 2009. A combination of hand-held models and computer imaging programs helps students answer oral questions about molecular structure and function: a controlled investigation of student learning. Cell Biol. Ed. 8(1):29-43

Herman, Tim, Colton, Shannon and Franzen, Margaret. 2008. Rethinking Outreach: Teaching the Process of Science through Modeling. PLoS Biology 6(4):e86

Herman, T., Morris, J., Colton, S. Batiza, A., Patrick, M., Franzen, M. and Goodsell, D.S. 2006. Tactile Teaching: Exploring Protein Structure/Function using Physical Models. Biochem. Molec. Biol. Educ. 34:247-254.

Bain, G., Yi, J., Beikmohamadi, M., Herman, T. and Patrick, M. 2006. Using physical models to teach concepts of biochemical structure and structure depiction in the introductory chemistry laboratory. J. Chem. Educ. 83(9):1322-1324. Supplements.

Roberts, J.R., Hagedorn, E., Dillenburg, P., Patrick, M. and Herman, T. Physical models enhance molecular three-dimensional literacy in an introductory biochemistry course. Biochem. Molec. Biol. Educ. 33(2):105-110. 2005

Put Your Lab in a Different Class. Sally Goodman, Nature 420, 12-14 (2002)

Images of Anthrax: A Team Approach. Jon Knopp, Chem Matters, December 2002, pages 4-6

Models of Excitement: Teachers use rapid prototyping to build protein structures. Toni Shears, HHMI Bulletin June 2002, pages 46-47