BioJava:CookBook:AAPROP:absorbanceandextinctioncoefficient
How are Absorbance and Extinction Coefficient computed?
Extinction Coefficient
Extinct(Prot) = (Tyr count)*Ext(Tyr) + (Trp count)*Ext(Trp) + (Cys count)*Ext(Cys) where Ext(Tyr) = 1490, Ext(Trp) = 5500, Ext(Cys) = 125
Absorbance
Absorb(Prot) = Extinct(Prot) / Molecular_Weight
There is a boolean parameter to be set - assumeCysReduced.
If assumeCysReduced is set to true, (Cys count) will always be 0.
If assumeCysReduced is set to false, Every pair of Cystine will be
counted as 1.
Our approach is based on
here.