A Visual Language for Protein Design

Handle URI:
http://hdl.handle.net/10754/625328
Title:
A Visual Language for Protein Design
Authors:
Cox, Robert Sidney ( 0000-0002-2009-6236 ) ; McLaughlin, James Alastair; Grunberg, Raik; Beal, Jacob; Wipat, Anil; Sauro, Herbert M.
Abstract:
As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in a
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Cox RS, McLaughlin JA, Grünberg R, Beal J, Wipat A, et al. (2017) A Visual Language for Protein Design. ACS Synthetic Biology 6: 1120–1123. Available: http://dx.doi.org/10.1021/acssynbio.6b00286.
Publisher:
American Chemical Society (ACS)
Journal:
ACS Synthetic Biology
Issue Date:
8-Feb-2017
DOI:
10.1021/acssynbio.6b00286
Type:
Article
ISSN:
2161-5063; 2161-5063
Sponsors:
The authors thank Steven Schkolne for consultation on glyph design and Matthew Pocock and Christopher Voigt for helpful discussions. J.A.M. is supported by FUJIFILM DioSynth Technologies. A.W. is supported by the Engineering and Physical Sciences Research Council grant EP/J02175X/1 and EP/N031962/1. RS.C. is supported in part by US DoD grant FA5209-16-P-0041 and National Science Foundation grant DBI-1355909. J.S.B. is supported in part by the National Science Foundation Expeditions in Computing Program Award #1522074 as part of the Living Computing Project. This document does not contain technology or technical data controlled under either the U.S. International Traffic in Arms Regulations or the U.S. Export Administration Regulations.
Additional Links:
http://pubs.acs.org/doi/full/10.1021/acssynbio.6b00286
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorCox, Robert Sidneyen
dc.contributor.authorMcLaughlin, James Alastairen
dc.contributor.authorGrunberg, Raiken
dc.contributor.authorBeal, Jacoben
dc.contributor.authorWipat, Anilen
dc.contributor.authorSauro, Herbert M.en
dc.date.accessioned2017-08-14T06:41:37Z-
dc.date.available2017-08-14T06:41:37Z-
dc.date.issued2017-02-08en
dc.identifier.citationCox RS, McLaughlin JA, Grünberg R, Beal J, Wipat A, et al. (2017) A Visual Language for Protein Design. ACS Synthetic Biology 6: 1120–1123. Available: http://dx.doi.org/10.1021/acssynbio.6b00286.en
dc.identifier.issn2161-5063en
dc.identifier.issn2161-5063en
dc.identifier.doi10.1021/acssynbio.6b00286en
dc.identifier.urihttp://hdl.handle.net/10754/625328-
dc.description.abstractAs protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in aen
dc.description.sponsorshipThe authors thank Steven Schkolne for consultation on glyph design and Matthew Pocock and Christopher Voigt for helpful discussions. J.A.M. is supported by FUJIFILM DioSynth Technologies. A.W. is supported by the Engineering and Physical Sciences Research Council grant EP/J02175X/1 and EP/N031962/1. RS.C. is supported in part by US DoD grant FA5209-16-P-0041 and National Science Foundation grant DBI-1355909. J.S.B. is supported in part by the National Science Foundation Expeditions in Computing Program Award #1522074 as part of the Living Computing Project. This document does not contain technology or technical data controlled under either the U.S. International Traffic in Arms Regulations or the U.S. Export Administration Regulations.en
dc.publisherAmerican Chemical Society (ACS)en
dc.relation.urlhttp://pubs.acs.org/doi/full/10.1021/acssynbio.6b00286en
dc.rightsThis is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.en
dc.rights.urihttp://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.htmlen
dc.subjectsynthetic biologyen
dc.subjectvisualizationen
dc.subjectSynthetic Biology Open Languageen
dc.subjectgenetic circuitsen
dc.subjectprotein engineeringen
dc.titleA Visual Language for Protein Designen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalACS Synthetic Biologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionMaterial Science Institute, University of Oregon, Eugene, OR, 97403, , United Statesen
dc.contributor.institutionSchool of Computing Science, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, , United Kingdomen
dc.contributor.institutionRaytheon BBN Technologies, Cambridge, MA, 02138, , , United Statesen
dc.contributor.institutionDepartment of Bioengineering, University of Washington, Seattle, WA, 98105, , United Statesen
kaust.authorGrunberg, Raiken
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