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Incorrect extinction coefficient for oxidized Cys #766
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Doesn't this method take care of that? biojava/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java Line 194 in 359dce8
It does seem to count N_cys/2. Would you be able to add a test case to demonstrate the issue? There's actually a test here (it uses the expasy server as the standard of truth): biojava/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java Line 211 in 359dce8
Perhaps you can add those new test cases to that test? |
From Pace et al, 1995:
Note that only cystine, the historical term for a disulfide bond, contributes to absorption. The method org.biojava.nbio.aaproperties.PeptidePropertiesImpl#getExtinctionCoefficient uses the cystEine (Cys) count. It is an easy mistake to make; the code comments even reference "Ext(Cystine) = 125".
Assuming complete S-S cross linking occurs, the correct number of disulfide bonds should be 'N_cys / 2' (integer math, quotient only). Using this count then establishes consistency with ExPASy (https://web.expasy.org/protparam/).
Some test cases that can be replicated with protparam:
Sequence: CCCCC
Ext. coefficient: 250
Sequence: CCCCCC
Ext. coefficient: 375
Sequence: CCCCCCC
Ext. coefficient: 375
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