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Protein Engineering, Vol 8, 999-1009, Copyright 1995 by Oxford University Press
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S Miyazawa
Faculty of Technology, Gunma University, Japan.
Probabilities of all possible correspondences of residues in aligning two
proteins are evaluated by assuming that the statistical weight of each
alignment is proportional to the exponent of its total similarity score.
Based on such probabilities, a probability alignment that includes the most
probable correspondences is proposed. In the case of highly similar
sequence pairs, the probability alignments agree with the maximum
similarity alignments that correspond to the alignments with the maximum
similarity score. Significant correspondences in the probability alignments
are those whose probabilities are > 0.5. The probability alignment
method is applied to a few protein pairs, and results indicate that such
highly probable correspondences in the probability alignments are probably
correct correspondences that agree with the structural alignments and that
incorrect correspondences in the maximum similarity alignments are usually
insignificant correspondences in the probability alignments. The root mean
square deviations in superimposition of corresponding residues tend to be
smaller for significant correspondences in the probability alignments than
for all correspondences in the maximum similarity alignments, indicating
that incorrect correspondences in the maximum similarity alignments tend to
be insignificant correspondences in probability alignments. This fact is
also confirmed in 109 protein pairs that are similar to each other with
sequence identities between 90 and 35%. In addition, the probability
alignment method may better predict correct correspondences than the
maximum similarity alignment method. Probability alignments do, of course,
depend on a scoring scheme but are less sensitive to the value of
parameters such as gap penalties. The present probability alignment method
is useful for constructing reliable alignments based on the probabilities
of correspondences and can be used with any scoring scheme.
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![]() ![]() S. Miyazawa and R. L. Jernigan Identifying sequence-structure pairs undetected by sequence alignments Protein Eng., July 1, 2000; 13(7): 459 - 475. [Abstract] [Full Text] [PDF] ![]() |
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