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.'' | ||
[[Image: | <table cellpadding=5 border=1 style="border-collapse:collapse;"><tr><td> | ||
[[Image:Phipsi-AH.gif|right]] | |||
* ''' | * '''Definitions 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]. | |||
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[[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): | |||
::* 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) | |||
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[[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><tr><td bgcolor="#f0f0f0"> | |||
* '''[[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. | ||
** A regular page in Proteopedia. | ** A regular page in Proteopedia. | ||
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[[Image:Ramachandran-jsmol.png|right|180px]] | |||
* '''The [[Ramachandran Plot]]''' | * '''The [[Ramachandran Plot]]''' | ||
** A regular page in Proteopedia. Featured in an article in Biochemistry and Molecular Biology Education, 2010. | ** 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''. | ** Extensive description with instructions on ''how to display the Ramachandran plot for any protein structure''. | ||
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[[Image:Ramachandran-inspection-AH.png|right|200px]] | |||
* '''[[Tutorial:Ramachandran_Plot_Inspection|Ramachandran Plot Inspection]]''' | * '''[[Tutorial:Ramachandran_Plot_Inspection|Ramachandran Plot Inspection]]''' | ||
** A special "Tutorial" page in Proteopedia (by [[User:Angel_Herraez|Angel Herráez]]) and an equivalent [http://biomodel.uah.es/model1j/prot/Ramachandran.htm page in Spanish] | ** A special "Tutorial" page in Proteopedia (by [[User:Angel_Herraez|Angel Herráez]]) and an equivalent [http://biomodel.uah.es/model1j/prot/Ramachandran.htm 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. | ** 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''. | ** You can display phi and psi for ''any pair of amino acids in any protein structure''. | ||
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[[Image:Dihedral-angles-anim.gif|right]] | <table align="right"><tr><td style="background:white;"> | ||
[[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]]''' | * '''[[Tutorial:Ramachandran_principle_and_phi_psi_angles|The Ramachandran Principle, Phi (φ) and Psi (ψ) Angles in Proteins]]''' | ||
** A special "Tutorial" page in Proteopedia (by [[User:Eric_Martz|Eric Martz]]) | ** A special "Tutorial" page in Proteopedia (by [[User:Eric_Martz|Eric Martz]]) | ||
** That tutorial repurposed as a '''slideshow''' with animated images (a Google Docs presentation): | ** That tutorial repurposed as a '''slideshow''' with animated images (a Google Docs presentation): | ||
*** [http://tinyurl.com/RamachandranPrinciple | *** [http://tinyurl.com/RamachandranPrinciple Slideshow] in English including explanation of dihedral angles with animated illustration | ||
*** [http://tinyurl.com/PrincipioRamachandran | *** [http://tinyurl.com/PrincipioRamachandran Slideshow] in Spanish | ||
** The slideshow is also available as a '''[https://tinyurl.com/RamachandranPrincipleYoutube YouTube Video]''' (in English), including explanation of dihedral angles with animated illustration. | ** The slideshow is also available as a '''[https://tinyurl.com/RamachandranPrincipleYoutube YouTube Video]''' (in English), including explanation of dihedral angles with animated illustration.<imagemap> | ||
Image:Youtube.png | |||
default [http://tinyurl.com/RamachandranPrincipleYoutube] | |||
</imagemap> | |||
** A '''quiz''' to self-assess understanding of the tutorial or the slideshow: | ** A '''quiz''' to self-assess understanding of the tutorial or the slideshow: | ||
*** [[Dihedral/Ramachandran_Principle_Quiz| | *** [[Dihedral/Ramachandran_Principle_Quiz|Quiz in English]] | ||
*** [[Dihedral/Ramachandran_Principle_Quiz (Spanish)| | *** [[Dihedral/Ramachandran_Principle_Quiz (Spanish)|Quiz in Spanish]] | ||
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* [http://clfs690.alivetek.org/CLFS690/amino/animballjmol.htm Another animation] of phi and psi angles connected to a Ramachandran plot (by David Jollie) | * [http://clfs690.alivetek.org/CLFS690/amino/animballjmol.htm Another animation] of phi and psi angles connected to a Ramachandran plot (by David Jollie) | ||
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* [[Ramachandran outlier]] showcases a special case where a residue is not conforming to the favored values in the Ramachandran plot. | * [[Ramachandran outlier]] showcases a special case where a residue is not conforming to the favored values in the Ramachandran plot. | ||
</td></tr></table> | |||
Latest revision as of 02:08, 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.
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