| 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);