Equivalent amino acids for similarity searches

Conrad Halling chhall at bb1t.monsanto.com
Tue Mar 22 13:46:54 EST 1994

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

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