| title | BioJava:CookBook3:ModFinder |
|---|---|
| permalink | wiki/BioJava%3ACookBook3%3AModFinder |
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.
Set<ModifiedCompound> identifyAllModfications(Structure struc) {
ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
parser.identify(struc);
Set`<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
return mcs;
} 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?](/wiki/BioJava:CookBook3:SupportedProtMod "wikilink")
- [How can I define a new protein
modification?](/wiki/BioJava:CookBook3:AddProtMod "wikilink")
</div>