How can I identify protein modifications in a structure?

BioJava provide a module biojava3-modfinder for identification of protein pre-, co-, and post-translational modifications from structures. A list of protein modifications has been pre-loaded. It is possible to identify all pre-loaded modifications or part of them.

Example: identify and print all preloaded modifications from a structure

Set<ModifiedCompound> identifyAllModfications(Structure struc) {

   ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
   parser.identify(struc);
   Set`<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
   return mcs;

}

Example: identify phosphorylation sites in a structure

```java List identifyPhosphosites(Structure struc) {

  List<ResidueNumber> phosphosites = new ArrayList`();   ProteinModificationIdentifier parser = new ProteinModificationIdentifier();   parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));   Set` mcs = parser.getIdentifiedModifiedCompound();   for (ModifiedCompound mc : mcs) {`       Set` groups = mc.getGroups(true);       for (StructureGroup group : groups) {`           phosphosites.add(group.getPDBResidueNumber());       }`   }`   return phosphosites;

} ```

Demo code to run the above methods

```java import org.biojava.nbio.structure.ResidueNumber; import org.biojava.nbio.structure.Structure; import org.biojava.nbio.structure.io.PDBFileReader; import org.biojava.nbio.protmod.structure.ProteinModificationIdentifier;

public static void main(String[] args) {

  try {`
      PDBFileReader reader = new PDBFileReader();
      reader.setAutoFetch(true);

      // identify all modificaitons from PDB:1CAD and print them       String pdbId = "1CAD";       Structure struc = reader.getStructureById(pdbId);       Set mcs = identifyAllModfications(struc);       for (ModifiedCompound mc : mcs) {`           System.out.println(mc.toString());       }`

      // identify all phosphosites from PDB:3MVJ and print them       pdbId = "3MVJ";       struc = reader.getStructureById(pdbId);       List psites = identifyPhosphosites(struc);       for (ResidueNumber psite : psites) {`           System.out.println(psite.toString());       }`   } catch(Exception e) {`       e.printStackTrace();   }`

} ```

See also