Equivalent amino acids for similarity searches

Who Knows tang at tgevax.life.uiuc.edu
Tue Mar 22 14:29:21 EST 1994


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.

Dayhoff's table is widely used. I don't know the reference. But if you are
familiar with GCG paackage, you can find the score table somewhere in the 
package.



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