Equivalent amino acids for similarity searches

JONATHAN PARRISH jopa at ac.dal.ca
Wed Mar 23 07:17:20 EST 1994

In article <2mmfdp$t1n at usenet.INS.CWRU.Edu>, dy684 at cleveland.Freenet.Edu (Roberto Albinoni) writes:
> i am comparing the dna-derived amino acids sequences of two proteins in
> order to determine which residues may be most important to enzymatic
> function. 
> i wonder if someone to point me to appropriate references on which amino
> acids can be considered most similar based on their chemistry and function,
> and also how one can 'score' the similarity of two proteins based not only
> on identical residues, but also on amino acids which belong to the same
> chemical families.

A nice reference which covers a lot of the similarity aspects, and
making a good attempt at presenting them simultaneously (through
Venn diagrams and an extensive discussion) is 

"The Classification of Amino Acid Conservation" by William Taylor, 
in the Journal of Theoretical Biology vol. 119 p.205-218 (1986)

While he doesn't present a scoring matrix (and he does explain why) 
the paper refers to the Dayhoff matrix, from there you should be able to 
find citation references to other matrices.

Hope this helps

Jonathan Parrish
Department of Biochemistry
Dalhousie University
Halifax, N.S.

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