BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks
Abstract
Although non-canonical residues, caps, crosslinks, and nicks play an important role in the function of many DNA, RNA, proteins, and complexes, we do not fully understand how networks of non-canonical macromolecules generate behavior. One barrier is our limited formats, such as IUPAC, for abstractly describing macromolecules. To overcome this barrier, we developed BpForms and BcForms, a toolkit of ontologies, grammars, and software for abstracting the primary structure of polymers and complexes as combinations of residues, caps, crosslinks, and nicks. The toolkit can help quality control, exchange, and integrate information about the primary structure of macromolecules into fine-grained global networks of intracellular biochemistry.
Keywords
Cite
@article{arxiv.1903.10042,
title = {BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks},
author = {Paul F. Lang and Yassmine Chebaro and Xiaoyue Zheng and John A. P. Sekar and Bilal Shaikh and Darren A. Natale and Jonathan R. Karr},
journal= {arXiv preprint arXiv:1903.10042},
year = {2021}
}
Comments
21 pages, 4 figures, 2 boxes