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--- evoss [2018/07/19 22:36] – sean
+++ evoss [2018/07/19 22:58] – sean
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-==== Evo-SS-Package ====
+==== Evolu-sec package ====
-Evolu-sec-Package is a part of research project as “Modelling the evolution of protein secondary structure”.\\
+<html>
-Evo-SS-Package contains phylogenetic analysis tools based on an evolutionary model of secondary structure.
+<p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span
-Analysis focus on phylogenetic tree inference [**left-top**], evolutionary distance estimation [**left-bottom**], and ancestral secondary structure reconstruction [**right**].
+class=SpellE><span lang=EN-GB>Evolu</span></span><span lang=EN-GB>-sec package
-The research project abstract is provided in next session.
+is a part of research project as “Modelling the evolution of protein secondary
-The dataset for the model development and the software can be accessed in the [[http://bioinf.scmb.uq.edu.au/evoss#supplementary_data|“Supplementary Data”]] session.
+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>.
+Analysis focus 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 next session. The dataset for the model development and the software can be accessed in the [[http://bioinf.scmb.uq.edu.au/evoss#supplementary_data|“Supplementary Data”]] session.
 {{:research:evolusec.png}}
 \\
 ----
 ==== Research Project ====
-**Modelling the evolution of protein secondary structure**\\
+**Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity**\\
-[[http://bioinf.scmb.uq.edu.au/research/jhih_siang_sean_lai|Jhih-Siang Lai]], [[http://kobelab.biosci.uq.edu.au/wiki/|Bostjan Kobe]] and [[http://bioinf.scmb.uq.edu.au/research/mikael_boden|Mikael Bodén]]\\
+[[http://bioinf.scmb.uq.edu.au/research/jhih_siang_sean_lai|Jhih-Siang Lai]], [[https://www.rostlab.org/|Burkhard Rost
+]], [[http://kobelab.biosci.uq.edu.au/wiki/|Bostjan Kobe]] and [[http://bioinf.scmb.uq.edu.au/research/mikael_boden|Mikael Bodén]]\\
 [[http://www.scmb.uq.edu.au/|School of Chemistry and Molecular Biosciences]], [[http://www.uq.edu.au|The University of Queensland]]\\
 Contact: //[[js.lai@uqconnect.edu.au|Jhih-Siang Lai]]//
 **Abstract**\\
-Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, attempts to reconstruct extremely ancient proteins and phylogenetic analyses of remote homologues must deal with the sequence diversity that results from extended periods of evolutionary change. In the last twenty years, the number of protein structures in the Protein Data Bank has increased twenty-fold. Using the same principles pioneered by Dayhoff [1], we seize this wealth of structure data and develop a protein secondary structure evolutionary model, based on differences between discrete secondary structure states observed in modern proteins and those hypothesized in their immediate ancestors. We implement maximum likelihood-based phylogenetic inference tools based on our evolutionary model. We apply these tools to the sequence-diverse but structurally-conserved Toll/interleukin-1 receptor (TIR) domains [2] and show that the resulting clades in a phylogenetic tree are more consistent with their biological properties than those of the same inference based on an amino acid model. The approach also allows us to infer ancestral secondary structure [3,4,5]; we compare these predictions with those of structure homology modelling and sequence-based secondary structure predictors. The secondary structure evolutionary model extracts information not available from modern structures or the ancestral protein sequences alone. Our evolutionary model has the capacity to highlight relationships that are evolutionarily rooted in structure, and therefore complements the use of sequence-based phylogenetic analysis.\\
+<html>
+<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. 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. 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. 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>
+</html>
 ----
 ==== Supplementary Data ====
-Supplementary data for "**Modelling the evolution of protein secondary structure**" can be downloaded as\\ [[https://cloudstor.aarnet.edu.au/plus/index.php/s/lxuMi0nwv8mRuov|Dataset]] or [[https://cloudstor.aarnet.edu.au/plus/index.php/s/MbQRrsIp1txz27a|Software]], separately.\\
+Supplementary data for "**Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity**" can be downloaded as\\ [[https://cloudstor.aarnet.edu.au/plus/index.php/s/lxuMi0nwv8mRuov|Dataset]] or [[https://cloudstor.aarnet.edu.au/plus/index.php/s/MbQRrsIp1txz27a|Software]], separately.\\
 \\
 Package may be downloaded as single one archive as\\ [[https://cloudstor.aarnet.edu.au/plus/index.php/s/UgZbhzrNcgQtMkQ|Full package download]].\\