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Fig. 2 | Genome Biology

Fig. 2

From: BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks

Fig. 2

Overview of the BpForms-BcForms toolkit. The toolkit includes (a) extensible alphabets of DNA, RNA, and protein residues and 5 caps; (b) an ontology of crosslinks; (c) a grammar for composing polymers from residues, 5 caps, crosslinks, and nicks; (d) a grammar for composing complexes from polymers and crosslinks; software tools for validating descriptions of macromolecules, (e) calculating molecular properties of macromolecules, (f) exporting macromolecules to other formats and visualizing macromolecules; (g) protocols for integrating descriptions of macromolecules into omics, systems biology, and synthetic biology formats for networks, models, and genetic designs; and (h) multiple user interfaces. (c) The grammar (text) for describing polymers (image); the colored text illustrates how the grammar captures non-canonical residues (colored portions of the image). (d) The grammar (colored text) for describing complexes (image); the colored text illustrates how the grammar captures inter-subunit crosslinks (colored portion of image)

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