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Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests.

Ray WC, Rumpf RW, Sullivan B, Callahan N, Magliery T, Machiraju R, Wong B, Krzywinski M, Bartlett CW - BMC Proc (2014)

Bottom Line: The data was grounded in actual experimental results in triosephosphate isomerase(TIM) enzymes.Judges found valuable and novel contributions in each of the entries, including interesting ways to hierarchicalize the protein into domains of informational interaction, tools for simultaneously understanding both sequential and spatial order, and approaches for conveying some types of inter-residue dependencies.In this manuscript we document the problem presented to the contestants, summarize the biological contributions of their entries, and suggest opportunities that this work has highlighted for even more improved tools in the future.

View Article: PubMed Central - HTML - PubMed

Affiliation: Nationwide Children's Hospital, 575 Children's Crossroad, 43215, Columbus, OH, USA ; The Ohio State University, 100 W. 18th Ave, 43210, Columbus, OH, USA ; Contest Chairs.

ABSTRACT

Introduction: In 2011, the BioVis symposium of the IEEE VisWeek conferences inaugurated a new variety of data analysis contest. Aimed at fostering collaborations between computational scientists and biologists, the BioVis contest provided real data from biological domains with emerging visualization needs, in the hope that novel approaches would result in powerful new tools for the community. In 2011 and 2012 the theme of these contests was expression Quantitative Trait Locus analysis, within and across tissues respectively. In 2013 the topic was updated to protein sequence and mutation visualization.

Methods: The contest was framed in the context of a real protein with numerous mutations that had lost function, and the question posed "what minimal set of changes would you propose to rescue function, or how could you support a biologist attempting to answer that question?". The data was grounded in actual experimental results in triosephosphate isomerase(TIM) enzymes. Seven teams composed of 36 individuals submitted entries with proposed solutions and approaches to the challenge. Their contributions ranged from careful analysis of the visualization and analytical requirements for the problem through integration of existing tools for analyzing the context and consequences of protein mutations, to completely new tools addressing the problem.

Results: Judges found valuable and novel contributions in each of the entries, including interesting ways to hierarchicalize the protein into domains of informational interaction, tools for simultaneously understanding both sequential and spatial order, and approaches for conveying some types of inter-residue dependencies. In this manuscript we document the problem presented to the contestants, summarize the biological contributions of their entries, and suggest opportunities that this work has highlighted for even more improved tools in the future.

No MeSH data available.


RINalyzer in action. RINalyzer displays both canonical sequence and structure information, as well as an eponymous Residue Interaction Map showing inter-residue contacts displayed by different family members and providing insight into the conservation of residue interaction.
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Figure 6: RINalyzer in action. RINalyzer displays both canonical sequence and structure information, as well as an eponymous Residue Interaction Map showing inter-residue contacts displayed by different family members and providing insight into the conservation of residue interaction.

Mentions: Doncheva et al.[12] wrapped several traditional tools for understanding sequence and structure conservation, around the unique idea that changes in residue-residue contacts might explain functional deficits in mutant proteins. To support exploration of this phenomenon they developed the idea of a family Residue Interaction Network (RIN), which essentially visualizes structurally detectable residue-residue contacts in each member of a protein family for which there are known structures. From the RIN, shown interacting with other analysis features in Figure 6 it's easy to see where there are highly-conserved residue-contacts and networks of contacts in the family, enabling examination of the changes in a mutant to be considered in the context of how these changes might affect the highly conserved contacts. In addition to the Residue Interaction Network view, RINalyzer incorporates a sequence view, a map-like overview of secondary structural layout (Pro-Origami[19]), and a 3D molecular viewer, with feature selection synchronized between all of the views.


Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests.

Ray WC, Rumpf RW, Sullivan B, Callahan N, Magliery T, Machiraju R, Wong B, Krzywinski M, Bartlett CW - BMC Proc (2014)

RINalyzer in action. RINalyzer displays both canonical sequence and structure information, as well as an eponymous Residue Interaction Map showing inter-residue contacts displayed by different family members and providing insight into the conservation of residue interaction.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4155613&req=5

Figure 6: RINalyzer in action. RINalyzer displays both canonical sequence and structure information, as well as an eponymous Residue Interaction Map showing inter-residue contacts displayed by different family members and providing insight into the conservation of residue interaction.
Mentions: Doncheva et al.[12] wrapped several traditional tools for understanding sequence and structure conservation, around the unique idea that changes in residue-residue contacts might explain functional deficits in mutant proteins. To support exploration of this phenomenon they developed the idea of a family Residue Interaction Network (RIN), which essentially visualizes structurally detectable residue-residue contacts in each member of a protein family for which there are known structures. From the RIN, shown interacting with other analysis features in Figure 6 it's easy to see where there are highly-conserved residue-contacts and networks of contacts in the family, enabling examination of the changes in a mutant to be considered in the context of how these changes might affect the highly conserved contacts. In addition to the Residue Interaction Network view, RINalyzer incorporates a sequence view, a map-like overview of secondary structural layout (Pro-Origami[19]), and a 3D molecular viewer, with feature selection synchronized between all of the views.

Bottom Line: The data was grounded in actual experimental results in triosephosphate isomerase(TIM) enzymes.Judges found valuable and novel contributions in each of the entries, including interesting ways to hierarchicalize the protein into domains of informational interaction, tools for simultaneously understanding both sequential and spatial order, and approaches for conveying some types of inter-residue dependencies.In this manuscript we document the problem presented to the contestants, summarize the biological contributions of their entries, and suggest opportunities that this work has highlighted for even more improved tools in the future.

View Article: PubMed Central - HTML - PubMed

Affiliation: Nationwide Children's Hospital, 575 Children's Crossroad, 43215, Columbus, OH, USA ; The Ohio State University, 100 W. 18th Ave, 43210, Columbus, OH, USA ; Contest Chairs.

ABSTRACT

Introduction: In 2011, the BioVis symposium of the IEEE VisWeek conferences inaugurated a new variety of data analysis contest. Aimed at fostering collaborations between computational scientists and biologists, the BioVis contest provided real data from biological domains with emerging visualization needs, in the hope that novel approaches would result in powerful new tools for the community. In 2011 and 2012 the theme of these contests was expression Quantitative Trait Locus analysis, within and across tissues respectively. In 2013 the topic was updated to protein sequence and mutation visualization.

Methods: The contest was framed in the context of a real protein with numerous mutations that had lost function, and the question posed "what minimal set of changes would you propose to rescue function, or how could you support a biologist attempting to answer that question?". The data was grounded in actual experimental results in triosephosphate isomerase(TIM) enzymes. Seven teams composed of 36 individuals submitted entries with proposed solutions and approaches to the challenge. Their contributions ranged from careful analysis of the visualization and analytical requirements for the problem through integration of existing tools for analyzing the context and consequences of protein mutations, to completely new tools addressing the problem.

Results: Judges found valuable and novel contributions in each of the entries, including interesting ways to hierarchicalize the protein into domains of informational interaction, tools for simultaneously understanding both sequential and spatial order, and approaches for conveying some types of inter-residue dependencies. In this manuscript we document the problem presented to the contestants, summarize the biological contributions of their entries, and suggest opportunities that this work has highlighted for even more improved tools in the future.

No MeSH data available.