A Visual Language for Protein Design.
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/ .
Material Science Institute, University of Oregon , Eugene, Oregon 97403, United States.
Robert Sidney
0000-0002-2009-6236
RS
Cox
School of Computing Science, Newcastle University , Newcastle upon Tyne NE1 7RU, U.K.
James Alastair
JA
McLaughlin
Computational Bioscience Research Center, King Abdullah University for Science and Technology , Thuwal 23955, Saudi Arabia.
Raik
R
Grünberg
Raytheon BBN Technologies , Cambridge, Massachusetts 02138, United States.
Jacob
J
Beal
School of Computing Science, Newcastle University , Newcastle upon Tyne NE1 7RU, U.K.
Anil
A
Wipat
Department of Bioengineering, University of Washington , Seattle, Washington 98105, United States.
Herbert M
HM
Sauro
D017076:Computer-Aided Design; D008954:Models, Biological; D015202:Protein Engineering / Q000379:methods; D012984:Software; D058615:Synthetic Biology / Q000379:methods*
Synthetic Biology Open Language; genetic circuits; protein engineering; synthetic biology; visualization