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== | ||
<StructureSection load='' size='340' side='right' caption='MI: covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions' scene='85/857774/Molecularinteraction/1'> | <StructureSection load='' size='340' side='right' caption='MI: covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions' scene='85/857774/Molecularinteraction/1'> | ||
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====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).==== | ||
| - | + | # <scene name='86/864086/Product_complex/2'>Distinguishing between covalent and non-covalent interactions</scene>. <jmol> | |
<jmolRadioGroup> | <jmolRadioGroup> | ||
<item> | <item> | ||
<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> You can turn off the <jmol> | |
| - | + | <jmolCheckbox> | |
| - | + | <scriptWhenChecked>contact on</scriptWhenChecked> | |
| - | + | <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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