A tutorial for the structure modules of BioJava
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The protein structure modules of BioJava provide an API that allows to
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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.
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.
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