Ramachandran function

Case number:699969-994565
Topic:General
Opened by:Crashguard303
Status:Open
Type:Suggestion
Opened on:Thursday, February 21, 2013 - 19:29
Last modified:Monday, February 25, 2013 - 22:19

Hi, this is also a kind of question:
Does the rebuild function use the Ramachandran plot?
http://en.wikipedia.org/wiki/Ramachandran_plot

If not, maybe we could use it for guessing the secondary structure.
Just an idea, as there already are some scripts which form loops or sheets when they find certain amino-acids.

regards,
Alex

P.S.:
I still want to have a function to fetch and change dihedral angles of segments directly (some kind of alignment).
180° for each angle and position would create a straight backbone as it is in denovo puzzles.
Using those angles in Lua's fields(arrays) by them per each segment would offer indefinte saveslots!

(Thu, 02/21/2013 - 19:29  |  4 comments)


Joined: 08/24/2011

"I still want to have a function to fetch and change dihedral angles of segments directly" waw this! I want it too!

Joined: 09/18/2009
Groups: SETI.Germany

This issue is cross-related to this one:
http://fold.it/portal/node/992730

The dihedral angles are called φ (Phi), ψ (Psi) or ω (Omega):
http://en.wikipedia.org/wiki/Dihedral_angle

brow42's picture
User offline. Last seen 3 days 15 hours ago. Offline
Joined: 09/19/2011
Groups: None

I think it's clear that it does use data similar to the Ramachandran plot, but it could be more detailed....phi/psi for every possible pair of amino acids. It has to be stored in the resources directory somewhere.

It seems to me that the rebuild algorithm goes through the selected region in some order (bisection, random, or sequential. I suspect bisection since it always bends first in the middle). It picks a random phi/psi from the 2-D table for that AA pair and secondary structure. It does this repeatedly to AA pairs until it satisfies the boundary conditions or gives up. Before it gives up, it solves for some phi/psi angles in the change using inverse kinematics http://cnx.org/content/m11613/latest

Before accepting the solution, or perhaps as part of the inverse kinematics, in includes a penalty for any bands (and perhaps clashing, I'm not convinced rebuild uses clashing importance).

Also, bump on my own feedback here: http://fold.it/portal/node/992893

Joined: 09/18/2009
Groups: SETI.Germany

Thanks for this information ;)

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