Dihedral/Index

(Difference between revisions)

Revision as of 21:44, 14 July 2018

This in an index page pointing to several resources on these topics.

Simplified 3D models in JSmol that can be rotated with your mouse, and set to various dihedral angles: in English and Spanish.

Animated explanation identifying the 4 atoms for phi in a polypeptide, and rotating it clockwise (positive angles) and counter-clockwise (negative angles):

Dihedral angles in proteins: an interactive display of phi and psi dihedral angles using a model of a tripeptide.
- A regular page in Proteopedia.
- Simple presentation, featuring a 3D model with planes, clashes and animations.

Phi and Psi Angles: a more detailed, guided explanation of determination and display of angles in the 3D model.
- A regular page in Proteopedia.

The Ramachandran Plot
- A regular page in Proteopedia. Featured in an article in Biochemistry and Molecular Biology Education, 2010.
- Extensive description with instructions on how to display the Ramachandran plot for any protein structure.

Ramachandran Plot Inspection
- A special "Tutorial" page in Proteopedia (by Angel Herráez) and an equivalent page in Spanish
- Interactive Ramachandran plot with many controls and details, connecting the Ramachandran plot with the display on the 3D model. Includes planes, clashes and animations.
- You can display phi and psi for any pair of amino acids in any protein structure.

The Ramachandran Principle, Phi (φ) and Psi (ψ) Angles in Proteins
- A special "Tutorial" page in Proteopedia (by Eric Martz)
- That tutorial repurposed as a slideshow with animated images (a Google Docs presentation):
  - slideshow in English including explanation of dihedral angles with animated illustration
  - slideshow in Spanish
- The slideshow is also available as a YouTube Video (in English), including explanation of dihedral angles with animated illustration.
- A quiz to self-assess understanding of the tutorial or the slideshow:
  - quiz in English
  - quiz in Spanish

Another animation of phi and psi angles connected to a Ramachandran plot (by David Jollie)

Ramachandran outlier showcases a special case where a residue is not conforming to the favored values in the Ramachandran plot.

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 ** A regular page in Proteopedia.
 ** Simple presentation, featuring a 3D model with planes, clashes and animations.
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 * '''[[Phi and Psi Angles]]''': a more detailed, guided explanation of determination and display of angles in the 3D model.
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 ** A regular page in Proteopedia. Featured in an article in Biochemistry and Molecular Biology Education, 2010.
 ** Extensive description with instructions on ''how to display the Ramachandran plot for any protein structure''.
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+</td></tr><tr><td bgcolor="#f0f0f0">
 * '''[[Tutorial:Ramachandran_Plot_Inspection|Ramachandran Plot Inspection]]'''
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 *** [[Dihedral/Ramachandran_Principle_Quiz|quiz in English]]
 *** [[Dihedral/Ramachandran_Principle_Quiz (Spanish)|quiz in Spanish]]
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+</td></tr><tr><td bgcolor="#f0f0f0">
 * [http://clfs690.alivetek.org/CLFS690/amino/animballjmol.htm Another animation] of phi and psi angles connected to a Ramachandran plot (by David Jollie)