<h2 id="how-can-i-identify-protein-modifications-in-a-structure">How can I identify protein modifications in a structure?</h2>

<p>BioJava provide a module <em>biojava3-modfinder</em> for identification of

protein pre-, co-, and post-translational modifications from structures.

<a href="BioJava:CookBook3:SupportedProtMod" title="wikilink">A list of protein

modifications</a> has been

pre-loaded. It is possible to identify all pre-loaded modifications or

part of them.</p>

<h2 id="example-identify-and-print-all-preloaded-modifications-from-a-structure">Example: identify and print all preloaded modifications from a structure</h2>

<java> 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<residuenumber> identifyPhosphosites(Structure struc) {

`   List`<residuenumber>` phosphosites = new ArrayList`<residuenumber>`();`

`   ProteinModificationIdentifier parser = new ProteinModificationIdentifier();`

`   parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));`

`   Set`<modifiedcompound>` mcs = parser.getIdentifiedModifiedCompound();`

`   for (ModifiedCompound mc : mcs) {`

`       Set`<structuregroup>` 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`<modifiedcompound>` 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`<residuenumber>` psites = identifyPhosphosites(struc);`

`       for (ResidueNumber psite : psites) {`

`           System.out.println(psite.toString());`

`       }`

`   } catch(Exception e) {`

`       e.printStackTrace();`

`   }`

}

See also

--------

<div style="-moz-column-count:3; column-count:3;">

- [How can I get the list of supported protein

modifications?](BioJava:CookBook3:SupportedProtMod "wikilink")

- [How can I define a new protein

modification?](BioJava:CookBook3:AddProtMod "wikilink")