A tutorial for the protein 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. </td> </tr>

This tutorial is split into several chapters.

Chapter 1 - Quick Installation

Chapter 2 - First Steps

Chapter 3 - The 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 - Protein 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 - Bonds

Chapter 16 - Special Cases

Chapter 17 - Lists of PDB IDs and PDB status information.

Andreas Prlić

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.

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

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