Journal article
A Visual Language for Protein Design
ACS synthetic biology, Vol.6(7), pp.1120-1123
07/21/2017
DOI: 10.1021/acssynbio.6b00286
PMID: 28173698
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 "drag, and drop" interface for visualization and computer-aided-design of engineered proteins, as well as conversion of annotated protein sequences to Protein Language diagrams and figure export. Protein Designer can be accessed at http://biocad.ncl.ac.uk/protein-designer/.
Details
- Title: Subtitle
- A Visual Language for Protein Design
- Creators
- Robert Sidney Cox - University of OregonJames Alastair McLaughlin - Newcastle UniversityRaik Gruenberg - King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Thuwal 23955, Saudi ArabiaJacob Beal - RTXAnil Wipat - Newcastle UniversityHerbert M. Sauro - University of Washington
- Resource Type
- Journal article
- Publication Details
- ACS synthetic biology, Vol.6(7), pp.1120-1123
- Publisher
- Amer Chemical Soc
- DOI
- 10.1021/acssynbio.6b00286
- PMID
- 28173698
- ISSN
- 2161-5063
- eISSN
- 2161-5063
- Number of pages
- 4
- Grant note
- 1522074 / National Science Foundation Expeditions in Computing Program Award of the Living Computing Project FUJIFILM DioSynth Technologies EP/N031962/1; EP/J02175X/1 / Engineering and Physical Sciences Research Council; UK Research & Innovation (UKRI); Engineering & Physical Sciences Research Council (EPSRC) DBI-1355909 / National Science Foundation grant; National Science Foundation (NSF) EP/J02175X/1; EP/N031962/1 / EPSRC; UK Research & Innovation (UKRI); Engineering & Physical Sciences Research Council (EPSRC) FA5209-16-P-0041 / US DoD grant; United States Department of Defense EP/J02175X/1; EP/N031962/1 / Engineering and Physical Sciences Research Council; UK Research & Innovation (UKRI); Engineering & Physical Sciences Research Council (EPSRC) 1522074 / Division of Computing and Communication Foundations; Direct For Computer & Info Scie & Enginr; National Science Foundation (NSF); NSF - Directorate for Computer & Information Science & Engineering (CISE)
- Language
- English
- Date published
- 07/21/2017
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627244902771
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