Journal:BAMBEd:A practical guide to teaching with Proteopedia

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A practical guide to teaching with Proteopedia

Claudia Castro, R. Jeremy Johnson, Bruno Kieffer, John A. Means, Ann Taylor, Jason Telford, Lynmarie K. Thompson, Joel L. Sussman, Jaime Prilusky, Karsten Theis [1][2]

About the paper on BAMBEd

The guide provides practical advice on how to use Proteopedia as an effective tool for teaching science students. Using eleven example lessons, we show how students can learn about specific biomolecules and to explore principles of molecular structure and functions. These lessons help students acquire skills such as gaining familiarity with conventions of biomolecular visualization, utilizing technical terms that are employed in biochemistry, correlating structural features with function, and developing strategies to tackle the complexity of biomacromolecules by interacting with 3D representations of them.

Interactive and Downloadable material for the BAMBEd paper

Type Goals Extent
Supplement Figure S1 Interactive 3D scenes Selected Proteopedia scenes from the activities described in this guide (scenes are either created by students or used in assignments).
Supplement S2 Biochem for Medicine students focus on process instead of knowledge; 3D structure of proteins and their relationship to their function one week
Supplement S3 Biochem I to investigate the structure, function, and dynamics of HIV protease. homework and in-class session
Supplement S4 Biochem lab independent learning pre-lab
Supplement S5 Biochem I evaluate 3D figures 3 class sessions
Supplement S6 Biochem II to have students develop their own stories relating protein structure and function. semester
Supplement S7 Structural Biology for Engineers support flipped classroom, produce rather than consume information, appreciate open questions semester
Supplement S8 Biochem I make clear connections between the structure and function of biological macromolecules semester
Supplement S9 Biochem appreciation for the structural nuances of proteins and structure determination method semester
Supplement S10 Biochem information literacy semester
Supplement S11 Biochem I deeper understanding of 2D figures in publications two 3-hour labs
Supplement S12 Biochem I become familiar with 3D, increase depth of engagement with subject matter semester


  1. Castro C, Johnson RJ, Kieffer B, Means JA, Taylor A, Telford J, Thompson LK, Sussman JL, Prilusky J, Theis K. A practical guide to teaching with Proteopedia. Biochem Mol Biol Educ. 2021 Jun 3. doi: 10.1002/bmb.21548. PMID:34080750 doi:
  2. A practical guide to teaching with Proteopedia (limited sharing)

Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky

This page complements a publication in scientific journals and is one of the Proteopedia's Interactive 3D Complement pages. For aditional details please see I3DC.
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