BioJava:CookBook3:SupportedProtMod
From BioJava
How can I get the list of supported protein modifications?
The protmod module contains an XML file, defining a list of protein modifications, retrieved from Protein Data Bank Chemical Component Dictrionary, RESID, and PSI-MOD. It contains many common modifications such glycosylation, phosphorylation, acelytation, methylation, etc. Crosslinks are also included, such disulfide bonds and iso-peptide bonds.
The protmod maintains a registry of supported protein modifications. The list of protein modifications contained in the XML file will be automatically loaded. You can define and register a new protein modification if it has not been defined in the XML file. From the protein modification registry, a user can retrieve
- all protein modifications,
- a protein modification by ID,
- a set of protein modifications by RESID ID,
- a set of protein modifications by PSI-MOD ID,
- a set of protein modifications by PDBCC ID,
- a set of protein modifications by category (attachment, modified residue, crosslink1, crosslink2, ..., crosslink7),
- a set of protein modifications by occurrence type (natural or hypothetical),
- a set of protein modifications by a keyword (glycoprotein, phosphoprotein, sulfoprotein, ...),
- a set of protein modifications by involved components.
Example: retrieve registered protein modifications
// a protein modification by ID ProteinModification mod = ProteinModificationRegistry.getById("0001"); Set<ProteinModification> mods; // all protein modifications mods = ProteinModificationRegistry.allModifications(); // a set of protein modifications by RESID ID mods = ProteinModificationRegistry.getByResidId("AA0151"); // a set of protein modifications by PSI-MOD ID mods = ProteinModificationRegistry.getByPsimodId("MOD:00305"); // a set of protein modifications by PDBCC ID mods = ProteinModificationRegistry.getByPdbccId("SEP"); // a set of protein modifications by category mods = ProteinModificationRegistry.getByCategory(ModificationCategory.ATTACHMENT); // a set of protein modifications by occurrence type mods = ProteinModificationRegistry.getByOccurrenceType(ModificationOccurrenceType.NATURAL); // a set of protein modifications by a keyword mods = ProteinModificationRegistry.getByKeyword("phosphoprotein"); // a set of protein modifications by involved components. mods = ProteinModificationRegistry.getByComponent(Component.of("FAD"));
