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--- evolusec [2018/10/09 15:58] – [Evolu-sec package] sean
+++ evolusec [2020/08/13 01:34] (current) – sean
@@ Line 3: / Line 3: @@
 <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
+forms part of a research project, reported in “Evolutionary model of protein secondary structure capable of revealing new biological relationships”.<o:p></o:p><a href="https://doi.org/10.1002/prot.25898">http://dx.doi.org/10.1101/563452</a></span></p>
-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
@@ Line 21: / Line 19: @@
 ----
 ==== Research Project ====
-**Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity**\\
+**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]]\\
@@ Line 51: / Line 49: @@
 ----
 ==== 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\\ [[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.\\
+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)]].\\
@@ Line 153: / Line 151: @@
 ----
+==== Application ====
+The Evolu-sec was applied for analysing the structural divergence of Toll/interleukin-1 receptor domains further including plant RUN1 TIR domain and human SARM1 TIR domain, published in
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+<div class=WordSection1>
+<p class=MsoNormal><a name="_GoBack"></a>"NAD<sup>+</sup> cleavage activity by
+animal and plant TIR domains in cell death pathways, <i>Science</i>, 365, 6455,
+."</p>
+<p class=MsoNormal><span lang=EN-GB><a
+href="http://www.doi.org/10.1126/science.aax1911">http://www.doi.org/10.1126/science.aax1911</a></span></p>
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+</div>
+</body>
+</html>
+This wiki page provides images of better resolution, which have been included in the supplementary dataset of "NAD+ cleavage activity by animal and plant TIR domains in cell death pathways".
+{{:research: TIR_science_tree1.png}}
+Figure 1. Unrooted phylogenetic tree of proteins containing TIR domains and structurally related domains. The phylogenetic tree includes 114 proteins from the intersection of DALI searches on human SARM1 TIR and plant RUN1 TIR. Only non-redundant proteins with structures at 4Å resolution or better and superpositions covering 125 residues or more in length were used. Numbers on branches are standard bootstrap values by resampling 100 times. Sub-trees are coloured to indicate kingdom and broad function and annotated with Gene Ontology terms that are statistically enriched for the group of proteins at the leaves. Each leaf specifies PDB and UniProt identifiers, protein and gene names; in addition, the absolute number of mutated amino acids and the ratio of missing residues in the structure relative to the protein sequence are provided.
+{{:research: TIR_science_tree2.png}}
+Figure 2. The alternative tree visualisation of Figure 1. Tips in red, brown, green, blue, purple are mammalian TIR domains, bacterial TIR domains, plant TIR domains, enzymes, and response regulatory domains, respectively. The star and the circle highlight the plant RUN1 TIR and human SARM1 TIR structures, respectively.
 ==== External links ====
 [[https://www.researchgate.net/profile/Jhih_Siang_Lai|Sean in ResearchGate]]\\
 [[research:jhih_siang_sean_lai|Sean's profile]]\\
+[[https://orcid.org/0000-0001-5677-5890|Sean in ORCID]]\\