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:Molecular Dynamics|Molecular Dynamics (MD)]]''': The NMR structures of the <scene name='85/857774/Md/1'>dimeric C-terminal domain of HIV-1 capsid protein</scene> (PDB ID: 2kod) showing a distribution of structures accessible through dynamic conformational changes, particularly of the less ordered regions of the protein, shown in green. The animated GIF image illustrates various conformational states attainable by the structure. As an example of an assessment for MD1.01, students may be required to create a model using an NMR structure of the protein, overlay the states, and color each differently to allow them to identify the most flexible regions in the structure.
+'''[[:Category:Molecular Dynamics|Molecular Dynamics (MD)]]''': The NMR structures of the <scene name='85/857774/Md/1'>dimeric C-terminal domain of HIV-1 capsid protein </scene>(<jmol>
-:''MD1.01 Students can recognize that biological molecules have different conformations. (Novice, Amateur)''
-'''[[:Category:Molecular Interactions|Molecular Interactions (MI)]]''': The <scene name='85/857774/Molecularinteraction/1'>DNA binding motif of the lambda repressor protein (ribbons) is shown bound to the operator of lambda phage viral DNA</scene>(<jmol>
    <jmolCheckbox>
      <scriptWhenUnChecked>animation off; delay 1; model 1
@@ Line 102: / Line 97: @@
      <text>animation</text>
    </jmolCheckbox>
-</jmol>) (space-filling representation) (PDB ID: 1lmb). Noncovalent interactions occur between the repressor protein and the DNA, mediated largely through alpha-helices of the protein binding in the major groove of the viral DNA. An example of a MI1.02 assessment would require students to display and describe the interactions at the interface of the two macromolecules.
+</jmol>):
+(PDB ID: 2kod) showing a distribution of structures accessible through dynamic conformational changes, particularly of the less ordered regions of the protein, shown in green. The animated GIF image illustrates various conformational states attainable by the structure. As an example of an assessment for MD1.01, students may be required to create a model using an NMR structure of the protein, overlay the states, and color each differently to allow them to identify the most flexible regions in the structure.
+:''MD1.01 Students can recognize that biological molecules have different conformations. (Novice, Amateur)''
+'''[[:Category:Molecular Interactions|Molecular Interactions (MI)]]''': The <scene name='85/857774/Molecularinteraction/1'>DNA binding motif of the lambda repressor protein (ribbons) is shown bound to the operator of lambda phage viral DNA</scene> (space-filling representation) (PDB ID: 1lmb). Noncovalent interactions occur between the repressor protein and the DNA, mediated largely through alpha-helices of the protein binding in the major groove of the viral DNA. An example of a MI1.02 assessment would require students to display and describe the interactions at the interface of the two macromolecules.
 :''MI1.02 Students can identify the different non‐covalent interactions given a 3D structure. (Amateur)''