# A New Criterion and Method for Amino Acid Classification

**Source**: https://www.maths.tcd.ie/report_series/abstracts/tcdm0402.html
**Parent**: https://www.maths.tcd.ie/research/papers/

**A New Criterion and Method for Amino Acid Classification**

Many evolutionary changes of the amino
acid sequences in proteins are conservative:
the replacement of one amino acid by another residue
has a far greater chance of being accepted if the
two residues have similar properties. It is difficult,
however, to identify relevant physicochemical properties
that capture this similarity. In this paper we introduce
a criterion that determines similarity from an
evolutionary point of view. Our criterion is based
on the description of protein evolution by a Markov
process and the corresponding matrix of instantaneous
replacement rates. It is inspired by the conductance,
a quantity that reflects the strength of mixing in a
Markov process. Furthermore we introduce a method to
divide the twenty amino acid residues into subsets
that achieve good scores with our criterion.
The criterion has the time invariance property that
different time distances of the same amino acid
replacement rate matrix lead to the same grouping;
but different rate matrices lead to different groupings.
Therefore it can be used as an automated method to
compare matrices derived from consideration of
different types of proteins, or from parts of
proteins sharing different structural or functional
features. We present the groupings resulting from
two standard matrices used in sequence alignment
and phylogenetic tree estimation.