Dihedral/Index

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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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-[[Image:Dihedral-angles-anim.gif]][[Image:Rama-youtube-EM.gif|right]]
+[[Image:Dihedral-angles-anim.gif]][[Image:Rama-youtube-EM.gif]][[Image:Ramachandran plot general 100K.jpg|right|250px]]
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 * '''[[Tutorial:Ramachandran_principle_and_phi_psi_angles|The Ramachandran Principle, Phi (φ) and Psi (ψ) Angles in Proteins]]'''
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-default [[#Simulations: Protein Folding]]
+default [http://tinyurl.com/RamachandranPrincipleYoutube]
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