The limits of protein secondary structure prediction
accuracy from multiple sequence alignment
Robert B. Russell & Geoffrey J. Barton
From J. Mol. Biol, 234, 931-937, 1993.
Abstract
The expected best residue-by-residue accuracies for secondary
structure prediction from multiple protein sequence alignment
have been determined by an analysis of known protein structural
families.
The results show substantial variation is possible among
homologous protein structures, and that 100\% agreement is unlikely
between a consensus prediction and one member of a protein structural
family.
The study provides the range of agreement to be expected between a
perfect secondary structure prediction from a multiple alignment and
each protein within the alignment. The results of this study overcome
the difficulties inherent in the use of residue-by-residue accuracy
for assessing the quality of consensus secondary structure predictions.
The accuracies of recent consensus predictions for the annexins, SH2
domains and SH3 domains fall within the expected range for a perfect
prediction.