User:Karsten Theis/Molecular Interactions
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| - | [[User:Karsten Theis/Molecular Interactions|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. | + | [[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. |
==Competencies== | ==Competencies== | ||
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<script>anim off; delay 1.0; model 1</script> | <script>anim off; delay 1.0; model 1</script> | ||
<text>product</text> | <text>product</text> | ||
| - | <checked> | + | <checked>false</checked> |
</item> | </item> | ||
<item> | <item> | ||
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<script>anim fps 1; anim mode loop; anim on;</script> | <script>anim fps 1; anim mode loop; anim on;</script> | ||
<text>animate</text> | <text>animate</text> | ||
| - | <checked> | + | <checked>true</checked> |
</item> | </item> | ||
</jmolRadioGroup> | </jmolRadioGroup> | ||
</jmol> | </jmol> | ||
| - | # <jmol><jmolLink><script>script "/scripts/78/786673/Gal_normal/1.spt"; 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> | + | # <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> |
| - | # Predicting hydrogen bond donors or acceptors. | + | <jmolCheckbox> |
| - | # Explaining the electronic origin of the different non‐covalent interactions using appropriate 3D renderings. | + | <scriptWhenChecked>contact on</scriptWhenChecked> |
| - | # Ranking the relative strengths of covalent and non-covalent interactions in a given 3D rendering. | + | <scriptWhenUnchecked>contact off</scriptWhenUnchecked> |
| + | <checked>true</checked> | ||
| + | <text>contacts</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol> | ||
| + | # Predicting <scene name='86/864086/Atp/3'>hydrogen bond</scene> donors or acceptors. | ||
| + | # Explaining the <scene name='86/864093/Water/1'>electronic origin</scene> of the different non‐covalent interactions using <jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenUnChecked>isosurface off</scriptWhenUnChecked> | ||
| + | <scriptWhenchecked>select all; isosurface molecular map mep color translucent</scriptWhenchecked> | ||
| + | <checked>false</checked> | ||
| + | <text>appropriate 3D renderings</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>. | ||
| + | # 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.==== | ||
| - | + | # <scene name='86/864086/Solvent_exposed/1'>Identifying regions exposed or shielded from solvent within a biomolecule.</scene> You can turn off the <jmol> | |
| - | + | <jmolCheckbox> | |
| - | + | <scriptWhenChecked>display all</scriptWhenChecked> | |
| - | + | <scriptWhenUnchecked>hide protein</scriptWhenUnchecked> | |
| - | + | <checked>true</checked> | |
| - | + | <text>repressor</text> | |
| - | + | </jmolCheckbox> | |
| - | + | </jmol> | |
| - | + | # Identifying small molecules (e.g. solvent, salt ions, metals, detergents) in a local environment. | |
| - | + | # <scene name='86/864086/Domains/1'>Predicting the impact of small molecules in the local environment on a molecular interaction.</scene> | |
| - | + | # Predicting how the pKa of an ionizable group depends on its local environment. | |
| + | # Proposing changes to the local environment that would yield a desired change in a molecular interaction. | ||
| + | # Guessing, based on molecular visualization tools, which intermolecular force is most critical to stabilizing a given interaction. | ||
</StructureSection> | </StructureSection> | ||
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== References == | == References == | ||
<references/> | <references/> | ||
| + | |||
| + | [[Category: BioMolViz]] | ||
| + | [[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
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