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evolusec [2018/09/22 21:31] – [Supplementary Data] sean | evolusec [2020/08/13 01:34] (current) – sean | ||
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- | forms part of a research project, reported in “Modelling the evolution | + | forms part of a research project, reported in “Evolutionary model of protein secondary structure |
- | structure: a new phylogenetic metric suitable for assessing structural | + | |
- | similarity”.< | + | |
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- | The research project abstract is provided in the next section. The dataset for the model development and the software can be accessed in the [[http:// | + | The research project abstract is provided in the next section. The dataset |
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==== Research Project ==== | ==== Research Project ==== | ||
- | **Modelling the evolution | + | **Evolutionary model of protein secondary structure |
[[http:// | [[http:// | ||
]], [[http:// | ]], [[http:// | ||
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==== Supplementary Data ==== | ==== Supplementary Data ==== | ||
- | Supplementary data for "**Modelling the evolution | + | Supplementary data for "**Evolutionary model of protein secondary structure |
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Package may be downloaded as a single archive from\\ [[https:// | Package may be downloaded as a single archive from\\ [[https:// | ||
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+ | ==== Application ==== | ||
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+ | The Evolu-sec was applied for analysing the structural divergence of Toll/ | ||
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+ | animal and plant TIR domains in cell death pathways, < | ||
+ | 2019."</ | ||
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+ | href=" | ||
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+ | 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" | ||
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+ | {{: | ||
+ | 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, | ||
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+ | {{: | ||
+ | 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. | ||
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==== External links ==== | ==== External links ==== | ||
[[https:// | [[https:// | ||
[[research: | [[research: | ||
+ | [[https:// | ||