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BioJava_CookBook3_SupportedProtMod.md

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title BioJava:CookBook3:SupportedProtMod
permalink wiki/BioJava%3ACookBook3%3ASupportedProtMod

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

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"));

See also

- [How can I identify protein modifications in a structure](/wiki/BioJava:CookBook3:ProtMod "wikilink") - [How can I define a new protein modification?](/wiki/BioJava:CookBook3:AddProtMod "wikilink")