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Evolu-sec package
<html> <p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span class=SpellE><span lang=EN-GB>Evolu</span></span><span lang=EN-GB>-sec package forms part of a research project, reported in “Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity”.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span class=SpellE><span lang=EN-GB>Evolu</span></span><span lang=EN-GB>-sec package contains phylogenetic analysis tools based on an evolutionary model of secondary structure <b style='mso-bidi-font-weight:normal'>[centre, Table 1]</b>. The analysis focuses on phylogenetic tree inference <b style='mso-bidi-font-weight: normal'>[left]</b>, evolutionary distance estimation <b style='mso-bidi-font-weight: normal'>[top]</b>, and ancestral secondary structure reconstruction. <b style='mso-bidi-font-weight:normal'>[bottom and right]</b>.</span></p> </html>
The research project abstract is provided in the next section. The dataset for the model development and the software can be accessed in the “Supplementary Data” section.
Research Project
Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity
Jhih-Siang Lai, Burkhard Rost
, Bostjan Kobe and Mikael Bodén
School of Chemistry and Molecular Biosciences, The University of Queensland
Contact: Jhih-Siang Lai
Abstract
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<p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><a
name="_GoBack"></a><span lang=EN-GB>Ancestral sequence reconstruction has had
recent success in decoding the origins and the determinants of complex protein
functions. However, attempts to reconstruct ancient proteins and phylogenetic
analyses of remote homologues must handle extreme amino-acid sequence diversity
resulting from extended periods of evolutionary change [2]. We exploited the wealth
of protein structures in the Protein Data Bank (PDB) to develop an evolutionary
model based on protein secondary structure. The approach follows the
differences between discrete secondary structure states observed in modern
proteins and those hypothesised in their immediate ancestors [1]. Based on this new
evolutionary model, we implemented maximum likelihood-based phylogenetic
inference tools to reconstruct ancestral secondary structure. The predictive
accuracy from the use of the evolutionary model surpasses that of structure
comparative modelling and sequence-based prediction methods; the reconstruction
extracts information not available from modern structures or the ancestral
protein sequences alone [3,4,5]. Based on a phylogenetic analysis of a sequence-diverse
protein family, we showed that the model has the capacity to highlight
relationships that are evolutionarily rooted in structure and not evident in
sequence-based phylogenetic analysis.</span></p>
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Supplementary Data
Supplementary data for "Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity" can be downloaded from
Dataset or Software, separately.
Package may be downloaded as a single archive from
Full package download.
- (Ancestral secondary structure reconstruction) ASSR needs version MATLAB 8.2 (R2013b) or later.
- Please send feedback and questions to author.
References
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