From Proteopedia
proteopedia linkproteopedia linkMolecular Interactions is one of the 12 themes of the BioMolViz framework. Within the theme, there are two groups of competencies. This page provides exemplary 3D scenes that illustrate these competencies along with an explanation and sample questions.
Framework
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1. Predicting the existence of an interaction using structural information (i.e. atomic distances).
- 1.01 Distinguishing between covalent and non-covalent interactions.
- 1.02 Identifying the different non‐covalent interactions given a 3D structure.
- 1.03 Predicting hydrogen bond donors or acceptors.
- 1.04 Explaining the electronic origin of the different non‐covalent interactions using appropriate 3D renderings.
- 1.05 Ranking the relative strengths of covalent and non-covalent interactions in a given 3D rendering.
2. Evaluating the effect of the local environment on molecular interactions.
- 2.01 Identifying regions exposed or shielded from solvent within a biomolecule. (Novice)
- 2.02 Identifying small molecules in a local environment (e.g. solvent, salt ions, metals, detergents).
- 2.03 Predicting the impact of small molecules in the local environment on a molecular interaction.
- 2.04 Predicting how the pKa of an ionizable group depends on its local environment.
- 2.05 Proposing changes to the local environment that would yield a desired change in a molecular interaction.
- 2.06 Guessing, based on molecular visualization tools, which intermolecular force is most critical to stabilizing a given interaction.
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References
