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How to get a 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 Dictionary, 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.

Examples

// 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”));

Navigation: Home | Book 6: The ModFinder Modules | Chapter 2 - How to get a list of supported protein modifications

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