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Applying graph theory to protein structures: An Atlas of coiled coils

Research output: Contribution to journalArticle

Original languageEnglish
Article numberbty347
Pages (from-to)3316-3323
Number of pages8
JournalBioinformatics
Volume34
Issue number19
Early online date2 May 2018
DOIs
DateAccepted/In press - 23 Apr 2018
DateE-pub ahead of print - 2 May 2018
DatePublished (current) - 1 Oct 2018

Abstract

Motivation

To understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterised experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analysing this resource. Here, we use tools from graph theory to define an atlas classification scheme for automatically categorising certain protein substructures.
Results

Focusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein-protein interaction motifs, we present a suite of computational resources designed for analysing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the ‘dark matter’ of coiled-coil structures; i.e., those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design.
Availability

iSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.

    Structured keywords

  • BrisSynBio
  • Bristol BioDesign Institute

    Research areas

  • Synthetic Biology

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    Rights statement: This is the final published version of the article (version of record). It first appeared online via Oxford University Press at https://academic.oup.com/bioinformatics/article/34/19/3316/4990824 . Please refer to any applicable terms of use of the publisher.

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    Licence: CC BY

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