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Susume's picture
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Joined: 10/02/2011

It appears that the score function and the Ideal SS tool have different ideas about what makes a great helix. If you run Idealize SS on a helix, and then shake and wiggle it (assuming it has at least one end free), tokens pointed out to me that wiggle will make the helix shorter and fatter. The dots on the rama map will move down a little bit. Which is right, the "ideal" shape, or the higher-scoring one that wiggle likes?

I have also noticed, when using the rama map to make design puzzles, that my helices are always 17 or 16 residues long (or 21 if I make longer sheets). That makes the number of turns come out right for having the attached sheets fall in a plane. The helices in the Koga & Koga paper are all 18 or 14 residues long. If the curl of the helices is the same, it should take the same number of segments to get the right number of turns. If we are using the ideal loops they discovered for their paper to connect helices to sheets, why would our helices not be the same length?

gdnskye's picture
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Joined: 11/10/2008
Further to what Susume has

Further to what Susume has asked. If the helices are being optimized in a less than ideal shape. Would this a. Effect the final possible score? and b. Make the protein less likely fold in real life?

jeff101's picture
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Joined: 04/20/2012
Groups: Go Science
Does having different amino acids matter?

My guess is that the Ideal SS tool does not account for the amino acid type
but that wiggle and shake do account for the amino acid type, thus leading to
different phi,psi values for different amino acid types. Shake and wiggle might
also account for several nearby amino acids when determining the best phi,psi
values for a particular amino acid in the protein.

tokens's picture
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Joined: 11/28/2011
I don't think it has got

I don't think it has got anything to do with amino acid type. For example it happens when all the sidechains are alanine.

Susume's picture
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Joined: 10/02/2011
Improved Ideal SS

The Oct 6, 2016 release has an improved Ideal SS tool that starts helixes out shorter and fatter than they used to be, more like what the score function prefers. One effect of this is that it now takes 18 segs of helix (like the Koga paper designs) to turn enough for a sheet-helix-sheet motif, rather than 17 segs as I had been using up until now.

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