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| evoss [2018/07/19 22:49] – [Research Project] 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:// | ||
| {{: | {{: | ||
| \\ | \\ | ||
| Line 17: | Line 28: | ||
| **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. 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. | + | < |
| + | <p class=MsoNormal style=' | ||
| + | name=" | ||
| + | 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.</ | ||
| + | </ | ||
| ---- | ---- | ||
| ==== 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:// | ||