Equivalent amino acids for similarity searches

Eberhard von Kitzing vkitzing at sunny.MPImF-Heidelberg.mpg.de
Thu Mar 24 03:18:53 EST 1994


dy684 at cleveland.Freenet.Edu (Roberto Albinoni) posted:
>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.

You may consider:

%0 Journal Article
%A Argos, Patrick
%D 1992
%T The Language of Protein Folding: Many forked tongues
%J Computers in Chemistry
%V 16
%N 2
%P 93-102
%K protein folding, protein sequence, amino acids, similarity,


%0 Journal Article
%A Niefind, Karsten
%A Schomburg, Dietmar
%D 1991
%T Amino Acid Similarity Coefficients for Protein Modeling and Sequence
Alignment Derived from Main-chain Folding Angles
%J Journal of Molecular Biology
%V 219
%P 481-497
%K similarity matrix, main chain conformation

and the references cited therein.



Eberhard von Kitzing
Max-Planck-Institute for Medical Research
Postfach 10 38 20, D 69028 Heidelberg, FRG

Internet: vkitzing at sunny.MPImF-Heidelberg.mpg.de



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