Dihedral/Index: Difference between revisions

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


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<!--[[Image:Ramachandran plot general 100K.jpg|right|200px]]-->
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[[Image:Dihedral angles-AH.png|right|200px]]
[[Image:Dihedral angles-AH.png|right|200px]]


* '''Definition of phi and psi''':
* '''Definition of phi and psi''':
** Simplified 3D models in JSmol that can be rotated with your mouse, and set to various dihedral angles: [http://biomodel.uah.es/model5/prot/diedros_en.htm in English] and [http://biomodel.uah.es/model5/prot/diedros.htm Spanish].
:* Simplified 3D models in JSmol that can be rotated with your mouse, and set to various dihedral angles: [http://biomodel.uah.es/model5/prot/diedros_en.htm in English] and [http://biomodel.uah.es/model5/prot/diedros.htm Spanish].
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[[Image:Phi-rotation-EM.gif|right]]
[[Image:Phi-rotation-EM.gif|right]]
** 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]. (Dihedral at 1:52 - 3:10)
::* As a YouTube video [https://tinyurl.com/RamachandranPrincipleYoutube in English]. (Dihedral at 1:52 - 3:10)
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Revision as of 00:43, 15 July 2018

Dihedral angles in proteins and the Ramachandran plotDihedral angles in proteins and the Ramachandran plot

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

  • Definition of phi and psi:
  • 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.
  • 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.

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez, Eric Martz
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