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

  • Genome Biol. 2020 May 18;21(1):117. doi: 10.1186/s13059-020-02025-z.
Paul F Lang  1  2  3 ,  Yassmine Chebaro  1  2  4 ,  Xiaoyue Zheng  1  2 ,  John A P Sekar  1  2 ,  Bilal Shaikh  1  2 ,  Darren A Natale  5 ,  Jonathan R Karr  6  7
Affiliations
  • 1. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA.
  • 2. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA.
  • 3. Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
  • 4. Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Strasbourg, Illkirch, 67404, France.
  • 5. Protein Information Resource, Georgetown University Medical Center, Washington, DC, 20007, USA.
  • 6. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. [email protected].
  • 7. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. [email protected].
PMID: 32423472 DOI: 10.1186/s13059-020-02025-z
Abstract

Non-canonical residues, caps, crosslinks, and nicks are important to many functions of DNAs, RNAs, proteins, and complexes. However, we do not fully understand how networks of such non-canonical macromolecules generate behavior. One barrier is our limited formats for describing macromolecules. To overcome this barrier, we develop BpForms and BcForms, a toolkit for representing the primary structure of macromolecules as combinations of residues, caps, crosslinks, and nicks. The toolkit can help omics researchers perform quality control and exchange information about macromolecules, help systems biologists assemble global models of cells that encompass processes such as post-translational modification, and help bioengineers design cells.

Keywords
Crosslink; Format; Genome-scale; Macromolecule; Modification; Multiscale; Network; Proteoform; Residue; Software.