5. Ontology of crosslinksΒΆ
As of March 2020, the ontology of crosslinks contains 36 crosslinks between protein residues.
We developed the ontology based on entries in RESID which represent crosslinked dipeptides:
- We searched RESID for entries that represent crosslinked dipeptides.
- We identified the individual residues which participate in each dimer.
- We used ChemAxon Marvin to identify the atoms involved in each crosslink.
- We used Open Babel to determine the indices of these atoms in the canonical SMILES ordering of the atoms.
- We manually assigned an id and name to each crosslink.
We invite the community to help us curate additional crosslinks, including DNA-DNA, RNA-RNA, DNA-protein, and RNA-protein crosslinks. Please contact us at info@karrlab.org to get involved, or please submit additional crosslinks via GitHub pull requests or issues.