List secondary structure under "Segment Information" when tab on a segment

Case number:845833-2000701
Topic:Game: Display
Opened by:jeff101
Status:Open
Type:Suggestion
Opened on:Sunday, May 10, 2015 - 23:13
Last modified:Saturday, May 16, 2015 - 20:07

I think it would be helpful if when you tabbed on a segment and the "Segment Information" box appeared,
within this box it would show the segment's present assigned secondary structure (H=helix, E=sheet, or L=loop).

(Sun, 05/10/2015 - 23:13  |  6 comments)


jeff101's picture
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One could also include in the "Segment Information" box what "Reset Structures"
and "Auto Structures" would give for the present protein conformation.
Also, various programs can predict %helix, %sheet, and %loop
for each amino acid in a particular protein sequence.
I have even seen charts that list %helix, %sheet, and %loop
for each amino acid no matter what its surrounding sequence is.
Perhaps this information could be included in the "Segment Information" box as well.

https://fold.it/portal/node/986051 has related ideas.

Thanks!

jeff101's picture
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Below is some LUA code that lists the probability a particular amino acid
is helix, sheet, or coil independent of its surrounding sequence:

-- below data comes from p.301 Cantor & Schimmel's 
-- "Biophysical Chemistry Part I: The Conformation of Biological Macromolecules" 
-- ISBN=0-7167-1188-5 
--
-- aa1cs = 1-letter AA codes (upper case)
aa1cs={'A','C','D','E','F','G','H','I','K','L',
'M','N','P','Q','R','S','T','V','W','Y'}
--
-- aa1ss = 1-letter AA codes (lower case)
aa1ss={'a','c','d','e','f','g','h','i','k','l',
'm','n','p','q','r','s','t','v','w','y'}
--
-- aa3s = 3-letter AA codes
aa3s={'Ala','Cys','Asp','Glu','Phe','Gly','His','Ile','Lys','Leu',
'Met','Asn','Pro','Gln','Arg','Ser','Thr','Val','Trp','Tyr'}
--
-- fas = frequency helical
fas={0.522, 0.278, 0.351, 0.549, 0.402, 0.19, 0.446, 0.358, 0.383, 0.48, 
0.429, 0.263, 0.212, 0.421, 0.282, 0.282, 0.295, 0.409, 0.409, 0.22}
--
-- fbs = frequency beta
fbs={0.167, 0.222, 0.137, 0.044, 0.219, 0.138, 0.122, 0.274, 0.126, 0.209, 
0.286, 0.113, 0.106, 0.211, 0.154, 0.124, 0.205, 0.282, 0.203, 0.22}
--
-- fcs = frequency coil
fcs={0.311, 0.5, 0.514, 0.407, 0.378, 0.668, 0.432, 0.368, 0.491, 0.311, 
0.286, 0.624, 0.682, 0.368, 0.564, 0.594, 0.494, 0.309, 0.386, 0.56}
--
-- ideally, for each AA, tots=fas+fbs+fcs=1
tots={}
--
for i=1,20 do
   tots[i]=fas[i]+fbs[i]+fcs[i]
   print('for '..aa3s[i]..' ('..aa1cs[i]..'), fa='..fas[i]..', fb='..fbs[i]..', & fc='..fcs[i]..' total to '..tots[i])  
end -- for I
jeff101's picture
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http://books.google.com/books?id=Jb0fQH1Eto0C&q=301#v=snippet&q=Table%205-11%20and%20301&f=false
gives the chart (Table 5-11 on p.301) used in the LUA code above.

jeff101's picture
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The book above is from 1980, and its Table 5-11 uses data from a 1974 paper.
Has anyone seen more recent data like in Table 5-11?
Do the %helix, %sheet, and %loop differ between soluble and membrane proteins?

Thanks!

jeff101's picture
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http://fold.it/portal/node/998229#comment-28378
for example, gives SAM Server predictions for
helix, sheet, and loop likelihoods
for each amino acid in puzzle 951.

jeff101's picture
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I think the SAM Server can also output these helix, sheet, and loop likelihoods
as several columns of %helix, %sheet, and %loop numeric values.

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