evoss [bioinf]

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Evolu-sec package is a part of research project as “Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity”.
Evolu-sec package contains phylogenetic analysis tools based on an evolutionary model of secondary structure [center]. Analysis focus on phylogenetic tree inference [left], evolutionary distance estimation [top], and ancestral secondary structure reconstruction [bottom and right]. The research project abstract is provided in next session. The dataset for the model development and the software can be accessed in the “Supplementary Data” session.

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
<html> <a name="_GoBack"></a>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. </html>

Supplementary data for "Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity" can be downloaded as
Dataset or Software, separately.

Package may be downloaded as single one archive as
Full package download.
Package contents can be viewed here.
Supplementary document

(Ancestral secondary structure reconstruction) ASSR needs version MATLAB 8.2 (R2013b) or later.
Please feedback needs to the author.

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<![if !supportLists]>1.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Dayhoff M, Schwartz R and Orcutt B (1978), "A Model of Evolutionary Change in Proteins", In Atlas of protein sequence and structure. Vol. 5, pp. 345-352. National Biomedical Research Foundation Silver Spring, MD.<o:p></o:p>

<![if !supportLists]>2.     <![endif]>Ve<span lang=EN-US style='font-size: 10.0pt;font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'> T, Williams SJ and Kobe B (2015), "Structure and function of Toll/interleukin-1 receptor/resistance protein (TIR) domains", Apoptosis. Vol. 20(2), pp. 250-261.<o:p></o:p>

<![if !supportLists]>3.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Clifton BE and Jackson CJ (2016), "Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins", Cell Chem Biol. Vol. 23(2), pp. 236-245.<o:p></o:p>

<![if !supportLists]>4.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ and Ortlund EA (2016), "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space", Proc Natl Acad Sci U S A. Vol. 113(2), pp. 326-331.<o:p></o:p>

<![if !supportLists]>5.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Wilson C, Agafonov RV, Hoemberger M, Kutter S, Zorba A, Halpin J, Buosi V, Otten R, Waterman D, Theobald DL and Kern D (2015), "Using ancient protein kinases to unravel a modern cancer drug's mechanism", Science. Vol. 347(6224), pp. 882-886.<o:p></o:p>

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Last updated by — Jhih-Siang Lai 2017/07/11 21:53

Evolu-sec package

Research Project

Supplementary Data

References

External links

bioinf