<h2 id="how-can-i-define-a-new-protein-modification">How can I define a new protein modification?</h2>

<p>The protmod module automatically loads <a href="BioJava:CookBook3:SupportedProtMod" title="wikilink">a list of protein

modifications</a> 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.</p>

<h2 id="example-define-and-register-disulfide-bond-in-java-code">Example: define and register disulfide bond in Java code</h2>

<java> // define the involved components, in this case two cystines

(CYS) List<component> components = new ArrayList<component>(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

--------

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

- [How can I identify protein modifications in a

structure?](BioJava:CookBook3:ProtMod "wikilink")

- [How can I get the list of supported protein

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