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
Bibliographical noteKAUST Repository Item: Exported on 2020-10-01
Acknowledgements: 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.