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    A Visual Language for Protein Design

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    Type
    Article
    Authors
    Cox, Robert Sidney
    McLaughlin, James Alastair
    Grunberg, Raik
    Beal, Jacob
    Wipat, Anil
    Sauro, Herbert M.
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Computational Bioscience Research Center (CBRC)
    Date
    2017-03-07
    Online Publication Date
    2017-03-07
    Print Publication Date
    2017-07-21
    Permanent link to this record
    http://hdl.handle.net/10754/625328
    
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    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
    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.
    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.
    Publisher
    American Chemical Society (ACS)
    Journal
    ACS Synthetic Biology
    DOI
    10.1021/acssynbio.6b00286
    Additional Links
    http://pubs.acs.org/doi/full/10.1021/acssynbio.6b00286
    ae974a485f413a2113503eed53cd6c53
    10.1021/acssynbio.6b00286
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)

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