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

```java // a protein modification by ID ProteinModification mod = ProteinModificationRegistry.getById(“0001”);

Set 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”));

```

See also