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The Structure Modules of BioJava

A tutorial for the structure modules of BioJava


The protein structure modules of BioJava provide an API that allows to
  • Maintain local installations of PDB
  • Load structures and manipulate them
  • Perform standard analysis such as sequence and structure alignments
  • Visualize structures
This tutorial provides an overview of the most important functionalities.


This tutorial is split into several chapters.

Chapter 1 - Quick Installation

Chapter 2 - First Steps

Chapter 3 - The Structure Data Model, for the representation of macromolecular structures

Chapter 4 - Local Installations of PDB

Chapter 5 - The Chemical Component Dictionary

Chapter 6 - How to Work with mmCIF/PDBx Files

Chapter 7 - SEQRES and ATOM Records, mapping to Uniprot (SIFTs)

Chapter 8 - Structure Alignments

Chapter 9 - Biological Assemblies

Chapter 10 - External Databases like SCOP & CATH

Chapter 11 - Accessible Surface Areas

Chapter 12 - Contacts Within a Chain and between Chains

Chapter 13 - Finding all Interfaces in Crystal: Crystal Contacts

Chapter 14 - Protein Symmetry

Chapter 15 - Protein Secondary Structure

Chapter 16 - Bonds

Chapter 17 - Special Cases

Chapter 18 - Lists of PDB IDs and PDB Status Information


The content of this tutorial is available under the CC-BY license, available here.

Please Cite

BioJava 5: A community driven open-source bioinformatics library
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
PLOS Computational Biology (2019) 15 (2):e1006791.
doi pubmed

Navigation: Home | Book 3: The Structure Modules

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