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evoss [2018/07/19 22:44] – sean | evoss [2018/07/19 22:58] – sean | ||
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==== Evolu-sec package ==== | ==== Evolu-sec package ==== | ||
- | 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**]. | + | <p class=MsoNormal style=' |
- | Analysis focus on phylogenetic tree inference [**left**], evolutionary distance estimation [**top**], and ancestral secondary structure reconstruction [**bottom and right**]. | + | class=SpellE>< |
- | 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# | + | structure: a new phylogenetic metric suitable for assessing structural |
+ | similarity”.< | ||
+ | <p class=MsoNormal style=' | ||
+ | class=SpellE>< | ||
+ | contains phylogenetic analysis tools based on an evolutionary model of | ||
+ | secondary structure | ||
+ | Analysis focus on phylogenetic tree inference | ||
+ | normal'> | ||
+ | normal'> | ||
+ | style=' | ||
+ | </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:// | ||
{{: | {{: | ||
\\ | \\ | ||
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**Abstract**\\ | **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. | + | <p class=MsoNormal style=' |
- | We exploited the wealth of protein structures in the Protein Data Bank (PDB) to develop an evolutionary model based on protein secondary structure. | + | name=" |
- | The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesised in their immediate ancestors. | + | recent success in decoding the origins and the determinants of complex protein |
- | Based on this new evolutionary model, we implemented maximum likelihood-based phylogenetic inference tools to reconstruct ancestral secondary structure. | + | functions. However, attempts to reconstruct ancient proteins and phylogenetic |
- | 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. | + | analyses of remote homologues must handle extreme amino-acid sequence diversity |
- | 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. | + | 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.</ | ||
+ | </ | ||
---- | ---- | ||
==== Supplementary Data ==== | ==== Supplementary Data ==== | ||
- | Supplementary data for " | + | Supplementary data for " |
\\ | \\ | ||
Package may be downloaded as single one archive as\\ [[https:// | Package may be downloaded as single one archive as\\ [[https:// |