Evolu-sec package
forms part of a research project, reported in “Evolutionary model of protein secondary structure capable of revealing new biological relationships”.
Evolu-sec package contains phylogenetic analysis tools based on an evolutionary model of secondary structure [centre, Table 1]. The analysis focuses on phylogenetic tree inference [left], evolutionary distance estimation [top], and ancestral secondary structure reconstruction. [bottom and right].
The research project abstract is provided in the next section. The dataset (140.9MB) for the model development and the software can be accessed in the [[http://bioinf.scmb.uq.edu.au/evolusec#supplementary_data|“Supplementary Data”]] section. {{:research:evolusec.png}} \\ ---- ==== Research Project ==== **Evolutionary model of protein secondary structure capable of revealing new biological relationships**\\ [[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 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.
---- ==== Supplementary Data ==== Supplementary data for "**Evolutionary model of protein secondary structure capable of revealing new biological relationships**" can be downloaded from\\ [[https://cloudstor.aarnet.edu.au/plus/s/r9Sml5YC6jx6Wfn|Dataset (140.3 MB)]] or [[https://cloudstor.aarnet.edu.au/plus/s/Sp17tsX26sgOmlb|Software (617 KB)]], separately.\\ \\ Package may be downloaded as a single archive from\\ [[https://cloudstor.aarnet.edu.au/plus/s/IR7C4llrOhutlcs|Full package download (140.9 MB)]].\\ \\ * (Ancestral secondary structure reconstruction) ASSR needs version MATLAB 8.2 (R2013b) or later.\\ * Please send feedback and questions to [[js.lai@uqconnect.edu.au|author]]. ---- ==== References ====1.
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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
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"NAD+ cleavage activity by animal and plant TIR domains in cell death pathways, Science, 365, 6455, 2019."
http://www.doi.org/10.1126/science.aax1911