Peppy: A virtual reality environment for exploring the principles of polypeptide structure.

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dc.contributor.author Doak, David G en
dc.contributor.author Denyer, Gareth S en
dc.contributor.author Gerrard, Juliet en
dc.contributor.author Mackay, Joel P en
dc.contributor.author Allison, Jane en
dc.date.accessioned 2020-02-11T23:05:56Z en
dc.date.issued 2020-01 en
dc.identifier.issn 0961-8368 en
dc.identifier.uri http://hdl.handle.net/2292/49928 en
dc.description.abstract A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses. en
dc.format.medium Print-Electronic en
dc.language eng en
dc.relation.ispartofseries Protein science : a publication of the Protein Society en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.title Peppy: A virtual reality environment for exploring the principles of polypeptide structure. en
dc.type Journal Article en
dc.identifier.doi 10.1002/pro.3752 en
pubs.issue 1 en
pubs.begin-page 157 en
pubs.volume 29 en
dc.rights.holder Copyright: The author en
pubs.end-page 168 en
pubs.publication-status Published en
dc.rights.accessrights http://purl.org/eprint/accessRights/RestrictedAccess en
pubs.subtype Research Support, Non-U.S. Gov't en
pubs.subtype Journal Article en
pubs.elements-id 784835 en
pubs.org-id Science en
pubs.org-id Biological Sciences en
dc.identifier.eissn 1469-896X en
pubs.record-created-at-source-date 2019-10-18 en
pubs.dimensions-id 31622516 en


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