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Protein Engineering, Vol. 12, No. 9, 707-712, September 1999
© 1999 Oxford University Press

Towards more meaningful hierarchical classification of amino acid scoring matrices

Alex C.W. May1

Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, UK

Hierarchical classifications of the 20 amino acids according to residue relationships within scoring matrices have not hitherto been tested for reliability. In fact, testing here of the residue groupings obtained thus from 18 published matrices shows that they vary considerably in reliability. This behaviour gives a new insight then into the matrices with respect to the relationships between the amino acid scores contained therein. For example, other than the trivial grouping of the 20 amino acids, no reliable residue groupings are present in all 18 matrix amino acid hierarchical classifications. Hierarchical classification of the 18 scoring matrices themselves is investigated in terms of matrix representation and choice of similarity and dissimilarity measures for matrix comparison. There is no absolute standard against which to compare a matrix clustering, of course, but it is possible to assess the usefulness of a measure for the purpose in terms of the reliability of the calculated tree. Matrix representation is shown to be important. Finally, a novel two-step approach for hierarchical classification of the 18 amino acid scoring matrices is described.

Keywords: amino acid clustering/amino acid scoring matrix/hierarchical classification/tree diagram/validation

1 Present address: Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 lAA, UK. E-mail: amay{at}nimr.mrc.ac.uk


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