User:Karsten Theis/Molecular Interactions

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(New page: Molecular 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 illustrat...)
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[[Molecular 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.
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[[User:Karsten Theis/Molecular Interactions|Molecular Interactions]] is one of the 12 themes of the [https://biomolviz.org/framework/ BioMolViz framework]. The theme is about covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions. Within the theme, there are two groups of competencies. This page provides exemplary 3D scenes with questions that invoke these competencies.
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==Framework==
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<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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==Competencies==
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<StructureSection load='' size='340' side='right' caption='MI: covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions' scene='85/857774/Molecularinteraction/1'>
====1. Predicting the existence of an interaction using structural information (i.e. atomic distances).====
====1. Predicting the existence of an interaction using structural information (i.e. atomic distances).====
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* 1.01 Distinguishing between covalent and non-covalent interactions.
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# <scene name='86/864086/Product_complex/2'>Distinguishing between covalent and non-covalent interactions</scene>. <jmol>
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<jmolRadioGroup>
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* 1.02 Identifying the different non‐covalent interactions given a 3D structure.
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<item>
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<script>anim off; delay 1.0; model 1</script>
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* 1.03 Predicting hydrogen bond donors or acceptors.
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<text>product</text>
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<checked>false</checked>
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* 1.04 Explaining the electronic origin of the different non‐covalent interactions using appropriate 3D renderings.
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</item>
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<item>
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* 1.05 Ranking the relative strengths of covalent and non-covalent interactions in a given 3D rendering.
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<script>anim off; delay 1.0; model 2</script>
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<text>intermediate</text>
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<checked>false</checked>
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</item>
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<item>
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<script>anim fps 1; anim mode loop; anim on;</script>
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<text>animate</text>
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<checked>true</checked>
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</item>
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</jmolRadioGroup>
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</jmol>
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# <jmol><jmolLink><script>script "/scripts/78/786673/Gal_normal/1.spt"; model 1; ppdiaCaptionCmd = "changeCaption('The active site of the enzyme GAL (green) in complex with the sugar galactose (CPK color scheme), with short distances between protein and ligand shown as yellow-reddish pillows','white','black');";javascript @ppdiaCaptionCmd;</script><text>Identifying the different non‐covalent interactions given a 3D structure.</text></jmolLink></jmol> You can turn off the <jmol>
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<jmolCheckbox>
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<scriptWhenChecked>contact on</scriptWhenChecked>
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<scriptWhenUnchecked>contact off</scriptWhenUnchecked>
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<checked>true</checked>
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<text>contacts</text>
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</jmolCheckbox>
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</jmol>
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# Predicting <scene name='86/864086/Atp/3'>hydrogen bond</scene> donors or acceptors.
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# Explaining the <scene name='86/864093/Water/1'>electronic origin</scene> of the different non‐covalent interactions using <jmol>
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<jmolCheckbox>
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<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
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<scriptWhenchecked>select all; isosurface molecular map mep color translucent</scriptWhenchecked>
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<checked>false</checked>
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<text>appropriate 3D renderings</text>
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</jmolCheckbox>
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</jmol>.
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# Ranking the relative strengths of <scene name='78/786673/Gal_active_site/6'>covalent and non-covalent interactions</scene> in a given 3D rendering.
====2. Evaluating the effect of the local environment on molecular interactions.====
====2. Evaluating the effect of the local environment on molecular interactions.====
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* 2.01 Identifying regions exposed or shielded from solvent within a biomolecule. (Novice)
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# <scene name='86/864086/Solvent_exposed/1'>Identifying regions exposed or shielded from solvent within a biomolecule.</scene> You can turn off the <jmol>
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<jmolCheckbox>
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<scriptWhenChecked>display all</scriptWhenChecked>
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<scriptWhenUnchecked>hide protein</scriptWhenUnchecked>
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<checked>true</checked>
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<text>repressor</text>
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</jmolCheckbox>
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</jmol>
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# Identifying small molecules (e.g. solvent, salt ions, metals, detergents) in a local environment.
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# <scene name='86/864086/Domains/1'>Predicting the impact of small molecules in the local environment on a molecular interaction.</scene>
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# Predicting how the pKa of an ionizable group depends on its local environment.
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# Proposing changes to the local environment that would yield a desired change in a molecular interaction.
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# Guessing, based on molecular visualization tools, which intermolecular force is most critical to stabilizing a given interaction.
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* 2.02 Identifying small molecules in a local environment (e.g. solvent, salt ions, metals, detergents).
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</StructureSection>
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* 2.03 Predicting the impact of small molecules in the local environment on a molecular interaction.
 
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* 2.04 Predicting how the pKa of an ionizable group depends on its local environment.
 
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* 2.05 Proposing changes to the local environment that would yield a desired change in a molecular interaction.
 
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* 2.06 Guessing, based on molecular visualization tools, which intermolecular force is most critical to stabilizing a given interaction.
 
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</StructureSection>
 
== References ==
== References ==
<references/>
<references/>
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[[Category: BioMolViz]]
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[[Category: Molecular Interactions]]

Current revision

Molecular Interactions is one of the 12 themes of the BioMolViz framework. The theme is about covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions. Within the theme, there are two groups of competencies. This page provides exemplary 3D scenes with questions that invoke these competencies.

Competencies

MI: covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions

Drag the structure with the mouse to rotate

References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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