beta_helix Staff Lv 1
As requested in the last Scientist Chat , here is the sequence logo predicted by the SAM server:
H = helix
E = sheet
C = loop (or coil)
The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.
For example, the Valines at residues 7, 121 & 128 are predicted to be part of a sheet. However, the Valines at residues 36, 91, 102, 113 & 141-142 are highly predicted to be part of a helix!
The above predictions are already on the starting model (based on the horizontal lines in the above figure).
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Cutaway view hint:
If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.
