Dihedral/Index
From Proteopedia
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** Animated explanation identifying the 4 atoms for phi in a polypeptide, and rotating it clockwise (positive angles) and counter-clockwise (negative angles): | ** Animated explanation identifying the 4 atoms for phi in a polypeptide, and rotating it clockwise (positive angles) and counter-clockwise (negative angles): | ||
*** As a slideshow [http://tinyurl.com/RamachandranPrinciple in English] and [http://tinyurl.com/PrincipioRamachandran in Spanish]. | *** As a slideshow [http://tinyurl.com/RamachandranPrinciple in English] and [http://tinyurl.com/PrincipioRamachandran in Spanish]. | ||
| - | *** As a YouTube video [https://tinyurl.com/RamachandranPrincipleYoutube in English]. | + | *** As a YouTube video [https://tinyurl.com/RamachandranPrincipleYoutube in English]. (Dihedral at 1:52 - 3:10) |
| - | </td></tr>< | + | </td></tr><tr><td> |
| + | [[Image:Dihedral-AH.gif|right]] | ||
* '''[[Dihedral/Dihedral_angles_in_proteins|Dihedral angles in proteins]]''': an interactive display of phi and psi dihedral angles using a model of a tripeptide. | * '''[[Dihedral/Dihedral_angles_in_proteins|Dihedral angles in proteins]]''': an interactive display of phi and psi dihedral angles using a model of a tripeptide. | ||
** A regular page in Proteopedia. | ** A regular page in Proteopedia. | ||
** Simple presentation, featuring a 3D model with planes, clashes and animations. | ** Simple presentation, featuring a 3D model with planes, clashes and animations. | ||
| + | </td></tr></table> | ||
* '''[[Phi and Psi Angles]]''': a more detailed, guided explanation of determination and display of angles in the 3D model. | * '''[[Phi and Psi Angles]]''': a more detailed, guided explanation of determination and display of angles in the 3D model. | ||
Revision as of 21:28, 14 July 2018
Dihedral angles in proteins and the Ramachandran plot
This in an index page pointing to several resources on these topics.
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- 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):
- 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:
- 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.
