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"; 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> | + | # <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> |
| - | # <scene name='86/864086/Atp/3'> | + | <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.==== | ||
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</jmol> | </jmol> | ||
# Identifying small molecules (e.g. solvent, salt ions, metals, detergents) in a local environment. | # Identifying small molecules (e.g. solvent, salt ions, metals, detergents) in a local environment. | ||
| - | # Predicting the impact of small molecules in the local environment on a molecular interaction. | + | # <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. | # 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. | # Proposing changes to the local environment that would yield a desired change in a molecular interaction. | ||
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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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