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

Chapter 8 - Protein Structure Alignments

Chapter 9 - Biological Assemblies

Chapter 10 - Protein Symmetry

Chapter 11 - Bonds

Andreas Prlić