Convergent evolution in structural elements of proteins investigated using cross profile analysis |
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Authors: | Kentaro Tomii Yoshito Sawada Shinya Honda |
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Institution: | (1) Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto Ward, Tokyo 135-0064, Japan;(2) Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Central 6, Tsukuba 305-8566, Japan |
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Abstract: | Background Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples
of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based
classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess
local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure
relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary
information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation
of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications
of protein segments. |
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