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/ .
Highlights
Protein engineering is one of the oldest disciplines of molecular biotechnology, with a rich history of engineering by mutation and fusion of genes coding for functional protein sequences
Protein Language has been simultaneously developed with the aim of compatibility with other standards in biological engineering, including the Systems Biology Graphical Notation (SBGN)[5] and the Synthetic Biology Open Language Visual (SBOLv).[6,7]
We have presented the first diagram language for constructing visualizations for purposes of protein engineering
Summary
Protein engineering is one of the oldest disciplines of molecular biotechnology, with a rich history of engineering by mutation and fusion of genes coding for functional protein sequences. As more sophisticated and model-driven methods have become available, practitioners need to communicate increasingly complex designs. In other disciplines, such as electrical engineering[1,2] or architecture and mechanical engineering,[3,4] standard visual symbols and diagram languages allow engineers to more comprehend designs, avoid mistakes, build software tools, etc. Protein Language is intended to aid protein design and not to describe all existing knowledge of protein biology This approach is in keeping with other visual languages in engineering disciplines: for example, electronics diagrams do not aim to capture the full range of electromagnetic phenomena and architectural diagrams do not aim to describe the full physics of built structures. We plan for Protein Language and its symbols to be adjusted and further refined through the experience of practitioners and an open community standardization process
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