OpenStructure: an integrated software framework for computational structural biology

Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):701-9. doi: 10.1107/S0907444913007051. Epub 2013 Apr 19.


Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from

Keywords: OpenStructure; computational structural biology.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Dengue Virus / enzymology
  • Methyltransferases / chemistry
  • Molecular Structure
  • Programming Languages
  • Proteomics / methods
  • Sequence Alignment
  • Software*
  • Urease / chemistry
  • User-Computer Interface


  • Methyltransferases
  • Urease