Category:BioMolViz: Difference between revisions

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== Overarching Themes in the BioMolViz Framework: ==

*'''Atomic Geometry (AG)''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

*'''[[: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.

*'''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.

*'''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.

*'''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.

*'''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.

== References: ==

~~<references/>~~

*Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

*Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.

~~<ref group='xtra'>PMID: 27486685</ref>~~

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.

@@ Line 3: / Line 3: @@
 == Overarching Themes in the BioMolViz Framework: ==
-*'''Atomic Geometry (AG)''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.
+*'''[[: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.
-*'''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.
-*'''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.
-*'''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.
-*'''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.
 == References: ==
-<references/>
+*Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.
-Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.
+*Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.
-<ref group='xtra'>PMID: 27486685</ref>
-Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.