How can I define a new protein modification?

The protmod module automatically loads a list of protein modifications into the protein modification registry. In case you have a protein modification that is not preloaded, it is possible to define it by yourself and add it into the registry.

Example: define and register disulfide bond in Java code

```java // define the involved components, in this case two cystines (CYS) List components = new ArrayList(2); components.add(Component.of("CYS")); components.add(Component.of("CYS"));

// define the atom linkages between the components, in this case the SG atoms on both CYS groups ModificationLinkage linkage = new ModificationLinkage(components, 0, “SG”, 1, “SG”);

// define the modification condition, i.e. what components are involved and what atoms are linked between them ModificationCondition condition = new ModificationConditionImpl(components, Collections.singletonList(linkage));

// build a modification ProteinModification mod =

       new ProteinModificationImpl.Builder("0018_test", 
       ModificationCategory.CROSS_LINK_2,
       ModificationOccurrenceType.NATURAL,
       condition)
       .setDescription("A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.")
       .setFormula("C 6 H 8 N 2 O 2 S 2")
       .setResidId("AA0025")
       .setResidName("L-cystine")
       .setPsimodId("MOD:00034")
       .setPsimodName("L-cystine (cross-link)")
       .setSystematicName("(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)")
       .addKeyword("disulfide bond")
       .addKeyword("redox-active center")
   .build();

//register the modification ProteinModificationRegistry.register(mod);

Example: definedisulfide bond in XML file and register by Java code
-------------------------------------------------------------------

<xml> <ProteinModifications>

`   `<Entry>  
`       `<Id>`0018`</Id>  
`       `<Description>`A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.`</Description>  
`       `<SystematicName>`(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)`</SystematicName>  
`       `<CrossReference>  
`           `

    RESID

`           `<Id>`AA0025`</Id>  
`           `<Name>`L-cystine`</Name>  
`       `</CrossReference>  
`       `<CrossReference>  
`           `

    PSI-MOD

`           `<Id>`MOD:00034`</Id>  
`           `<Name>`L-cystine (cross-link)`</Name>  
`       `</CrossReference>  
`       `<Condition>  
`           `<Component component="1">  
`               `<Id source="PDBCC">`CYS`</Id>  
`           `</Component>  
`           `<Component component="2">  
`               `<Id source="PDBCC">`CYS`</Id>  
`           `</Component>  
`           `<Bond>  
`               `<Atom component="1">`SG`</Atom>  
`               `<Atom component="2">`SG`</Atom>  
`           `</Bond>  
`       `</Condition>  
`       `<Occurrence>`natural`</Occurrence>  
`       `<Category>`crosslink2`</Category>  
`       `<Keyword>`redox-active center`</Keyword>  
`       `<Keyword>`disulfide bond`</Keyword>  
`   `</Entry>

</ProteinModifications> </xml>

```java FileInputStream fis = new FileInputStream("path/to/file");
ProteinModificationXmlReader.registerProteinModificationFromXml(fis);

See also