Biopython reference SASA values for 20 amino acids?
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8 weeks ago
Nick ▴ 40

Hi all,

Biopython implements the Shrake Rupley approximation for the solvent accessible surface area (SASA) of residues and atoms. I was wondering if there are reference values from Ala-X-Ala structures or even better "accepted" structures to compute the SASA with a specific parameterisation?

pdb structure biopython sasa • 339 views
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8 weeks ago
Mensur Dlakic ★ 27k

Values used by BioPython are somewhere in the code - shouldn't be difficult to find.

Rost & Sander, 1994 Proteins 20, 216:

A = 106
C = 135
D = 163
E = 194
F = 197
G = 84
H = 184
I = 169
K = 205
L = 164
M = 188
N = 157
P = 136
Q = 198
R = 248
S = 130
T = 142
V = 142
W = 227
Y = 222
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I don't think BioPython uses these values or I missed it. It was more about getting the relative SASA as correctly explained in the wiki article. This is great! Weird that this brilliant table didnt make it to my search results. It's not the same as having the structures to compute this yourself with a specific algorithm at hand but it is close enough!

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