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Book 6: ModFinder Module
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‎README.md‎

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Book 5: [The Protein-Disorder Module](protein-disorder/README.md), predicting protein-disorder.
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Book 6: [The ModFinder Module](modfinder/README.md), identifying potein modifications in 3D structures
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## License
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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.

‎modfinder/README.md‎

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The ModFinder Module of BioJava
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=====================================================
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A tutorial for the modfinder module of [BioJava](http://www.biojava.org)
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## About
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<table>
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<tr>
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<td>
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<img src='https://cloud.githubusercontent.com/assets/840895/22190971/fe5cd304-e0f4-11e6-9eb5-c1b071312081.png'>
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</td>
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<td>
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The <i>modfinder</i> module of BioJava provides an API The <i>alignment</i> module of BioJava provides an API for identification of protein pre-, co-, and post-translational modifications from structures.
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</td>
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</tr>
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</table>
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## Index
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This tutorial is split into several chapters.
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Chapter 1 - Quick [Installation](installation.md)
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Chapter 2 - [How to get the list of supported protein modifications](supported-protein-modifications.md)
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Chapter 3 - [How to identify protein modifications in a structure](identify-protein-modifications.md)
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Chapter 4 - [How to define a new protein modiifcation](add-protein-modification.md)
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## Please cite
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**BioJava: an open-source framework for bioinformatics in 2012**<br/>
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*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
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[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
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[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
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## License
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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
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[view license](../license.md)
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<!--automatically generated footer-->
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---
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Navigation:
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[Home](../README.md)
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| Book 6: The ModFinder Module
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Prev: [Book 5: The Protein-Disorder Module Module](../protein-disorder/README.md)

‎modfinder/add-protein-modification.md‎

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How to define a new protein modiifcation?
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===
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The protmod module automatically loads [a list of protein modifications](supported-protein-modifications.md) 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.
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## Example: define and register disulfide bond in java code
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```java
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// define the involved components, in this case two cystines (CYS)
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List components = new ArrayList(2);
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components.add(Component.of("CYS"));
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components.add(Component.of("CYS"));
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// define the atom linkages between the components, in this case the SG atoms on both CYS groups
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ModificationLinkage linkage = new ModificationLinkage(components, 0, “SG”, 1, “SG”);
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// define the modification condition, i.e. what components are involved and what atoms are linked between them
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ModificationCondition condition = new ModificationConditionImpl(components, Collections.singletonList(linkage));
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// build a modification
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ProteinModification mod =
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new ProteinModificationImpl.Builder("0018_test",
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ModificationCategory.CROSS_LINK_2,
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ModificationOccurrenceType.NATURAL,
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condition)
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.setDescription("A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.")
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.setFormula("C 6 H 8 N 2 O 2 S 2")
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.setResidId("AA0025")
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.setResidName("L-cystine")
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.setPsimodId("MOD:00034")
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.setPsimodName("L-cystine (cross-link)")
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.setSystematicName("(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)")
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.addKeyword("disulfide bond")
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.addKeyword("redox-active center")
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.build();
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//register the modification
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ProteinModificationRegistry.register(mod);
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```
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## Example: definedisulfide bond in xml file and register by java code
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```xml
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<ProteinModifications>
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<Entry>
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<Id>0018</Id>
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<Description>A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.</Description>
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<SystematicName>(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)</SystematicName>
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<CrossReference>
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<Source>RESID</Source>
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<Id>AA0025</Id>
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<Name>L-cystine</Name>
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</CrossReference>
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<CrossReference>
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<Source>PSI-MOD</Source>
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<Id>MOD:00034</Id>
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<Name>L-cystine (cross-link)</Name>
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</CrossReference>
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<Condition>
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<Component component="1">
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<Id source="PDBCC">CYS</Id>
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</Component>
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<Component component="2">
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<Id source="PDBCC">CYS</Id>
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</Component>
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<Bond>
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<Atom component="1">SG</Atom>
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<Atom component="2">SG</Atom>
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</Bond>
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</Condition>
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<Occurrence>natural</Occurrence>
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<Category>crosslink2</Category>
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<Keyword>redox-active center</Keyword>
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<Keyword>disulfide bond</Keyword>
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</Entry>
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</ProteinModifications>
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```
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```java
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FileInputStream fis = new FileInputStream("path/to/file");
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ProteinModificationXmlReader.registerProteinModificationFromXml(fis);
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```
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Navigation:
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[Home](../README.md)
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| [Book 6: The ModFinder Modules](README.md)
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| Chapter 4 - How to define a new protein modiifcation
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Prev: [Chapter 3 : How to identify protein modifications in a structure](identify-protein-modifications.md)
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‎modfinder/identify-protein-modifications.md‎

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How to identify protein modifications in a structure?
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===
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## Example: Identify and print all preloaded modifications from a structure
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```java
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Set<ModifiedCompound> identifyAllModfications(Structure struc) {
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ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
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parser.identify(struc);
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Set`<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
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return mcs;
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}
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```
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## Example: Identify phosphorylation sites in a structure
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```java
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List identifyPhosphosites(Structure struc) {
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List<ResidueNumber> phosphosites = new ArrayList`();
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ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
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parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));
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Set mcs = parser.getIdentifiedModifiedCompound();
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for (ModifiedCompound mc : mcs) {
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Set` groups = mc.getGroups(true);
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for (StructureGroup group : groups) {
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phosphosites.add(group.getPDBResidueNumber());
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}
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}
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return phosphosites;
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}
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```
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## Demo code to run the above methods
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```java
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import org.biojava.nbio.structure.ResidueNumber;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.io.PDBFileReader;
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import org.biojava.nbio.protmod.structure.ProteinModificationIdentifier;
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public static void main(String[] args) {
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try {`
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PDBFileReader reader = new PDBFileReader();
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reader.setAutoFetch(true);
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// identify all modificaitons from PDB:1CAD and print them
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String pdbId = "1CAD";
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Structure struc = reader.getStructureById(pdbId);
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Set mcs = identifyAllModfications(struc);
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for (ModifiedCompound mc : mcs) {
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System.out.println(mc.toString());
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}
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// identify all phosphosites from PDB:3MVJ and print them
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pdbId = "3MVJ";
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struc = reader.getStructureById(pdbId);
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List psites = identifyPhosphosites(struc);
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for (ResidueNumber psite : psites) {
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System.out.println(psite.toString());
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}
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} catch(Exception e) {
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e.printStackTrace();
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}
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}
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```
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Navigation:
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[Home](../README.md)
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| [Book 6: The ModFinder Modules](README.md)
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| Chapter 3 - How to identify protein modifications in a structure
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Prev: [Chapter 2 : How to get a list of supported protein modifications](supported-protein-modifications.md)
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Next: [Chapter 4 : How to define a new protein modiifcation](add-protein-modification.md)

‎modfinder/installation.md‎

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## Quick Installation
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In the beginning, just one quick paragraph of how to get access to BioJava.
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BioJava is open source and you can get the code from [Github](https://github.com/biojava/biojava), however it might be easier this way:
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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...
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<dependency>
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<!-- This imports the latest SNAPSHOT builds from the protein structure modules of BioJava.
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-->
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>4.2.0</version>
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</dependency>
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<dependency>
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<!-- This imports the latest SNAPSHOT builds from the protein modfinder modules of BioJava.
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-->
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<groupId>org.biojava</groupId>
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<artifactId>biojava-modfinder</artifactId>
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<version>4.2.0</version>
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</dependency>
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<!-- other biojava jars as needed -->
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</dependencies>
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```
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If you run
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<pre>
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mvn package
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</pre>
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on your project, the BioJava dependencies will be automatically downloaded and installed for you.
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<!--automatically generated footer-->
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---
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Navigation:
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[Home](../README.md)
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| [Book 6: The ModFinder Modules](README.md)
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| Chapter 1 : Installation
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Next: [Chapter 2 : How to get the list of supported protein modifications](supported-protein-modifications.md)

‎modfinder/supported-protein-modifications.md‎

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How to get a list of supported protein modifications?
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===
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The protmod module contains [an XML file](https://github.com/biojava/biojava/blob/master/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml), defining a list of protein modifications, retrieved from [Protein Data Bank Chemical Component Dictrionary](http://www.wwpdb.org/ccd.html), [RESID](http://pir.georgetown.edu/resid/), and [PSI-MOD](http://www.psidev.info/MOD). It contains many common modifications such glycosylation, phosphorylation, acelytation, methylation, etc. Crosslinks are also included, such disulfide bonds and iso-peptide bonds.
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The protmod maintains a registry of supported protein modifications. The list of protein modifications contained in the XML file will be automatically loaded. You can [define and register a new protein modification](add-protein-modification.md) if it has not been defined in the XML file. From the protein modification registry, a user can retrieve:
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- all protein modifications,
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- a protein modification by ID,
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- a set of protein modifications by RESID ID,
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- a set of protein modifications by PSI-MOD ID,
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- a set of protein modifications by PDBCC ID,
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- a set of protein modifications by category (attachment, modified residue, crosslink1, crosslink2, …, crosslink7),
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- a set of protein modifications by occurrence type (natural or hypothetical),
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- a set of protein modifications by a keyword (glycoprotein, phosphoprotein, sulfoprotein, …),
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- a set of protein modifications by involved components.
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## Examples
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```java
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// a protein modification by ID
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ProteinModification mod = ProteinModificationRegistry.getById(“0001”);
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Set mods;
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// all protein modifications
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mods = ProteinModificationRegistry.allModifications();
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// a set of protein modifications by RESID ID
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mods = ProteinModificationRegistry.getByResidId(“AA0151”);
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// a set of protein modifications by PSI-MOD ID
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mods = ProteinModificationRegistry.getByPsimodId(“MOD:00305”);
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// a set of protein modifications by PDBCC ID
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mods = ProteinModificationRegistry.getByPdbccId(“SEP”);
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// a set of protein modifications by category
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mods = ProteinModificationRegistry.getByCategory(ModificationCategory.ATTACHMENT);
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// a set of protein modifications by occurrence type
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mods = ProteinModificationRegistry.getByOccurrenceType(ModificationOccurrenceType.NATURAL);
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// a set of protein modifications by a keyword
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mods = ProteinModificationRegistry.getByKeyword(“phosphoprotein”);
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// a set of protein modifications by involved components.
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mods = ProteinModificationRegistry.getByComponent(Component.of(“FAD”));
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```
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Navigation:
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[Home](../README.md)
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| [Book 6: The ModFinder Modules](README.md)
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| Chapter 2 - How to get a list of supported protein modifications
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Prev: [Chapter 1 : Installation](installation.md)
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Next: [Chapter 3 : How to identify protein modifications in a structure](identify-protein-modifications.md)

‎protein-disorder/README.md‎

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| Book 3: The Protein Structure modules
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Prev: [Book 4: The Genomics Module](../genomics/README.md)
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| Next: [Book 6: The ModFinder Module](../modfinder/README.md)

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