Integrated visual analysis of protein structures, sequences, and feature data

BMC Bioinformatics
Christian StolteSeán I O'Donoghue

Abstract

To understand the molecular mechanisms that give rise to a protein's function, biologists often need to (i) find and access all related atomic-resolution 3D structures, and (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures. To streamline these processes we recently developed Aquaria, a resource offering unprecedented access to protein structure information based on an all-against-all comparison of SwissProt and PDB sequences. In this work, we provide a requirements analysis for several frequently occuring tasks in molecular biology and describe how design choices in Aquaria meet these requirements. Finally, we show how the interface can be used to explore features of a protein and gain biologically meaningful insights in two case studies conducted by domain experts. The user interface design of Aquaria enables biologists to gain unprecedented access to molecular structures and simplifies the generation of insight. The tasks involved in mapping sequence features onto structures can be conducted easier and faster using Aquaria.

References

Apr 9, 1999·Protein Engineering·B Rost
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Jul 26, 2005·Proteomics·Lennart MartensRolf Apweiler
Jul 14, 2006·BMC Bioinformatics·Elaine C MengThomas E Ferrin
Nov 28, 2008·Journal of Structural and Functional Genomics·Konstantin ArnoldTorsten Schwede
Oct 17, 2009·IEEE Transactions on Visualization and Computer Graphics·Julian Heinrich, Daniel Weiskopf
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Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
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Oct 24, 2014·Faraday Discussions·Julian HeinrichDaniel Weiskopf
Jan 31, 2015·Nature Methods·Seán I O'DonoghueAndrea Schafferhans

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Citations

Mar 3, 2017·BMC Bioinformatics·Lucia KocincováBarbora Kozlíková
Sep 4, 2015·BMC Bioinformatics·Jan AertsDaniel Weiskopf
Mar 21, 2020·Biochemical Society Transactions·Xavier MartinezMarc Baaden

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Methods Mentioned

BETA
NMR

Software Mentioned

ePMV viewer
SRS 3D
Aquaria 3D viewer
SRS3D
Photoshop
Blender viewer
UCSF Chimera
Adobe Illustrator
Adobe Photoshop
SignalP

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