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I have so far only seen programs that work on monomeric amino acidic (1D) sequences, like ProtParam, but now that more 3D protein structure predictions can be trusted, I wonder if there is an implementation of the calculation of a "protein extinction coefficent" that works on a PDB file as input, which could be a multimer (more than one chain).

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  • $\begingroup$ ProtParam estimates extinction coefficients solely by the number of tryptophan, tyrosine and cystine residues. It doesn’t matter whether your protein is oligomeric or not. Or are you asking if there is a more accurate algorithm that considers the microenvironments of aromatic residues based on structure? That I don’t know. $\endgroup$
    – canadianer
    Feb 1 at 2:26
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    $\begingroup$ Well, it might matter if your protein contained a prosthetic group that absorbs at the wavelength of interest: a haem group, for example (or a pyridoxal phosphate group) $\endgroup$
    – user338907
    Feb 1 at 15:34

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