The BioMolViz Project: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Kristen Procko, Josh Beckham, Jaime Prilusky, Karsten Theis

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 '''[[:Category:Atomic Geometry|Atomic Geometry (AG)]]''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.
-'''Alternate Renderings (AR)''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.
+'''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.
-'''Construction and Annotation (CA)''' ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.
+'''[[:Category:Construction and Annotation|Construction and Annotation (CA)]]''' ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.
-'''Ligands and Modifications (LM)''' ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.
+'''[[:Category:Ligands and Modifications|Ligands and Modifications (LM)]]''' ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.
-'''Macromolecular Assemblies (MA)''' ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.
+'''[[:Category:Macromolecular Assemblies|Macromolecular Assemblies (MA)]]''' ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.
-'''Macromolecular Building Blocks (MB)''' ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.
+''[[:Category:Macromolecular Building Blocks|Macromolecular Building Blocks (MB)]]''' ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.
-'''Molecular Dynamics (MD)''' ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.
+''[[:Category:Molecular Dynamics|Molecular Dynamics (MD)]]''' ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.
-'''Molecular Interactions (MI)''' ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.
+''[[:Category:Molecular Interactions|Molecular Interactions (MI)]]''' ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.
-'''Symmetry/Asymmetry Recognition (SA)''' ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.
+''[[:Category:Symmetry/Asymmetry Recognition|Symmetry/Asymmetry Recognition (SA)]]''' ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.
-'''Structure‐Function Relationship (SF)''' ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.
+''[[:Category:Structure‐Function Relationship|Structure‐Function Relationship (SF)]]''' ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.
-'''Structural Model Skepticism (SK)''' ‐ Recognition of the limitations of models to describe the structure of macromolecules.
+''[[:Category:Structural Model Skepticism|Structural Model Skepticism (SK)]]''' ‐ Recognition of the limitations of models to describe the structure of macromolecules.
-'''Topology and Connectivity (TC)''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.
+''[[:Category:Topology and Connectivity|Topology and Connectivity (TC)]]''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.
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 IN PROGRESS. Full example coming soon!
-The viewer may first wish to focus on a <scene name='86/865933/Unit_a/5'>single subunit of the complex</scene>. The <scene name='86/865933/Labeled_ligand/2'>ligand</scene> is shown as spacefilling in this model.
+As an example of the'''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' Overarching Theme learning goal, is AR1: “Students can create meaningful molecular images to convey features such as secondary structure, CPK coloring, active sites and molecular interactions.” A specific learning objective within this goal is AR1.04: “students can infer information from rendering a structure in different ways.”
+Given the structure of 5-methylthioribose 1-phosphate(MTRu-1-P) isomerase bound to MTRu-1-P (PDB ID: 2yvk chain A), use Jmol (or another molecular visualization tool such as Chimera or PyMOL) to identify the amino acids in the protein that interact with the ligand.
+To show mastery of this assessment, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>. The <scene name='86/865933/Labeled_ligand/2'>ligand</scene> is shown as spacefilling in this model.
 </StructureSection>
 == References ==
 <references/>