5. Ontology of crosslinks
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 email@example.com to get involved, or please submit additional crosslinks via GitHub pull requests or issues.