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Protein Engineering, Vol. 13, No. 8, 545-550, August 2000
© 2000 Oxford University Press

Structure-derived substitution matrices for alignment of distantly related sequences

Andreas Prlic, Francisco S. Domingues and Manfred J. Sippl1

Center of Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob-Haringerstrasse 3, A-5020 Salzburg, Austria

Sequence alignment is a standard method to infer evolutionary, structural, and functional relationships among sequences. The quality of alignments depends on the substitution matrix used. Here we derive matrices based on superimpositions from protein pairs of similar structure, but of low or no sequence similarity. In a performance test the matrices are compared with 12 other previously published matrices. It is found that the structure-derived matrices are applicable for comparisons of distantly related sequences. We investigate the influence of evolutionary relationships of protein pairs on the alignment accuracy.


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