Structure-derived substitution matrices for alignment of distantly related sequences

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 sequ...

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Bibliographic Details
Published inProtein engineering Vol. 13; no. 8; pp. 545 - 550
Main Authors Prlić, A, Domingues, F S, Sippl, M J
Format Journal Article
LanguageEnglish
Published England Oxford Publishing Limited (England) 01.08.2000
Subjects
Models, Molecular
Protein Conformation
Sequence Alignment - methods
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Summary: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.
ISSN:0269-2139
1741-0126
1741-0134
DOI:10.1093/protein/13.8.545