BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
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 macromolecul...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02025-z |
| _version_ | 1818328383047598080 |
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| author | Paul F. Lang Yassmine Chebaro Xiaoyue Zheng John A. P. Sekar Bilal Shaikh Darren A. Natale Jonathan R. Karr |
| author_facet | Paul F. Lang Yassmine Chebaro Xiaoyue Zheng John A. P. Sekar Bilal Shaikh Darren A. Natale Jonathan R. Karr |
| author_sort | Paul F. Lang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T12:31:17Z |
| format | Article |
| id | doaj.art-22daf2cdfc72467e9f4ac79ddb1bcf89 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-13T12:31:17Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-22daf2cdfc72467e9f4ac79ddb1bcf892022-12-21T23:46:01ZengBMCGenome Biology1474-760X2020-05-0121112110.1186/s13059-020-02025-zBpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networksPaul F. Lang0Yassmine Chebaro1Xiaoyue Zheng2John A. P. Sekar3Bilal Shaikh4Darren A. Natale5Jonathan R. Karr6Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount SinaiIcahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount SinaiIcahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount SinaiIcahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount SinaiIcahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount SinaiProtein Information Resource, Georgetown University Medical CenterIcahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount SinaiAbstract 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.http://link.springer.com/article/10.1186/s13059-020-02025-zFormatSoftwareMacromoleculeProteoformResidueModification |
| spellingShingle | Paul F. Lang Yassmine Chebaro Xiaoyue Zheng John A. P. Sekar Bilal Shaikh Darren A. Natale Jonathan R. Karr BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks Genome Biology Format Software Macromolecule Proteoform Residue Modification |
| title | BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks |
| title_full | BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks |
| title_fullStr | BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks |
| title_full_unstemmed | BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks |
| title_short | BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks |
| title_sort | bpforms and bcforms a toolkit for concretely describing non canonical polymers and complexes to facilitate global biochemical networks |
| topic | Format Software Macromolecule Proteoform Residue Modification |
| url | http://link.springer.com/article/10.1186/s13059-020-02025-z |
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