Category:BioMolViz

The goal of the BioMolecular Visualization Group (BioMolViz) is to promote molecular visualization literacy. This group of educators, assessment experts and biomolecular visualization enthusiasts began in 2012 to expand the Biomolecular Visualization Framework (Bateman and Craig 2010). The expanded Framework includes twelve ‘Overarching Themes’ (listed below), which are further expanded into learning goals and learning objectives (Dries et al. 2016). The group is currently developing a repository of assessments to measure molecular visualization literacy and welcomes input and engagement from the broader community. More information can be found on the BioMolViz website and here.

Overarching Themes in the BioMolViz Framework:Overarching Themes in the BioMolViz Framework:

• Atomic Geometry (AG) ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

• Alternate Renderings (AR) ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

• Construction and Annotation (CA) ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

• Ligands and Modifications (LM) ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

• Macromolecular Assemblies (MA) ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

• Macromolecular Building Blocks (MB) ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

• Molecular Dynamics (MD) ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

• Molecular Interactions (MI) ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

• Structural Model Skepticism (SK) ‐ Recognition of the limitations of models to describe the structure of macromolecules.

• Structure‐Function Relationship (SF) ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

• Symmetry/Asymmetry Recognition (SA) ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

• Topology and Connectivity (TC) ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

References:References:

• Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.
• Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.