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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


Andreas Prlić

Please cite

BioJava: an open-source framework for bioinformatics in 2012
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
Bioinformatics (2012) 28 (20): 2693-2695.
doi pubmed


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

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Navigation: Home | Book 3: The Structure Modules

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