Equivalent amino acids for similarity searches

[Conrad Halling]

In article <2mmfdp$t1n at usenet.INS.CWRU.Edu>, dy684 at cleveland.Freenet.Edu
(Roberto Albinoni) wrote:

> 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.

Start with the following reference:

Pearson, W. R.  1990.  Rapid and sensitive sequence comparison with FASTP
    and FASTA.  Methods Enzymol. 183:63-98.

Figure 3 in this paper displays the PAM250 scoring matrix, which was
"derived from the analysis of the amino acid replacements occurring among
related proteins and [which] specifies a range of positive scores for
replacements that commonly occur among related proteins and negative scores
for unlikely replacements" (above reference, p. 73).

-- 
Conrad Halling
Computational Molecular Biologist
Monsanto Co., St. Louis