pdb-l: Conservative amino acid substitutions

Kevin Karplus karplus at soe.ucsc.edu
Wed Feb 9 10:19:30 PST 2005


"conservative amino acid substitution" is not a well-defined term,
though the different usages are usually fairly close.  

One common operational definition is that the substitution matrix for
the pair of residues has a positive value.  This, of course, depends
on what substitution matrix one uses, and is not really very useful
when other methods for regularizing amino acid distributions are used.

Still, since the concept is of dividing substitutions into
conservative and non-conservative is inherently imposing a binary
classification on a more continuous space, you aren't going to be able
to get a perfect answer, and picking the positive pairs out of
BLOSUM50 is as good a choice as any.

------------------------------------------------------------
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
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