| title | BioJava:CookBook3:AddProtMod |
|---|---|
| permalink | wiki/BioJava%3ACookBook3%3AAddProtMod |
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.
(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);
0018
A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.
(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)
RESID
AA0025
L-cystine
PSI-MOD
MOD:00034
L-cystine (cross-link)
CYS
CYS
SG
SG
natural
crosslink2
redox-active center
disulfide bond
ProteinModificationXmlReader.registerProteinModificationFromXml(fis);