The ModFinder Module of BioJava
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A tutorial for the modfinder module of [BioJava](http://www.biojava.org)

## About
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            The <i>modfinder</i> module of BioJava provides an API for identification of protein pre-, co-, and post-translational modifications from structures.
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## Index

This tutorial is split into several chapters.

Chapter 1 - Quick [Installation](installation.md)

Chapter 2 - [How to get the list of supported protein modifications](supported-protein-modifications.md)

Chapter 3 - [How to identify protein modifications in a structure](identify-protein-modifications.md)

Chapter 4 - [How to define a new protein modification](add-protein-modification.md)

## License

The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](../license.md).

## Please Cite

**BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank**<br/>
*Jianjiong Gao; Andreas Prlic; Chunxiao Bi; Wolfgang F. Bluhm; Dimitris Dimitropoulos; Dong Xu; Philip E. Bourne; Peter W. Rose* <br/>
[Bioinformatics. 2017 Feb 17.](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx101) <br/>
[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtx101-blue.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btx101) [![pubmed](http://img.shields.io/badge/pubmed-28334105-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/28334105)

**BioJava 5: A community driven open-source bioinformatics library**<br/>
*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)



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