The BioMolViz Project

The twelve overarching themes of the Framework are outlined below, and the associated learning goals and objectives, can be viewed on the BioMolViz website.

Atomic Geometry (AG) ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes. As an example, is shown. A C-O-C bond angle in the sugar ring is shown, in addition to the dihedral/torsion angle of the center bond defined by four consecutive ring atoms (C-C-C-O). Viewers should be able to differentiate bond angles from dihedral/torsion angles and predict changes from ideal angles. An example assessment that encompasses objectives AG1.02, AG1.03, and AG1.04 would require students to measure the C-O-C bond angle, recognize that the ideal tetrahedral bond angle geometry is 109.5º and describe this deviation due to the chair conformation of the structure. An assessment that encompasses AG3.03 would require students to display and describe the atoms involved in measuring the dihedral angle.

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.

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

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

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

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