Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Oct 15;26(20):2626-8.
doi: 10.1093/bioinformatics/btq481. Epub 2010 Aug 23.

OpenStructure: a flexible software framework for computational structural biology

Marco Biasini  1 , Valerio Mariani, Jürgen Haas, Stefan Scheuber, Andreas D Schenk, Torsten Schwede, Ansgar Philippsen
Affiliations

OpenStructure: a flexible software framework for computational structural biology

Marco Biasini et al. Bioinformatics. .

Abstract

Motivation: Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms.

Availability: Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org.

Contact: torsten.schwede@unibas.ch

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Molecular surface representation of a SH2 domain (PDB:3IMJ) colored by conservation of the positions in a multiple sequence alignment. The color scale ranges from red for conserved residues to blue for residues with high variability. The ligand peptide is shown as yellow stick representation. The image was rendered in OpenStructure, the molecular surface was calculated using MSMS (Sanner et al., 1996). See Supplementary Table S1 for details on calculation of sequence conservation scores.
See this image and copyright information in PMC

References

    1. Arnold K, et al. The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics. 2006;22:195–201. - PubMed
    1. Arnold K, et al. The protein model portal. J. Struct. Funct. Genomics. 2009;10:1–8. - PMC - PubMed
    1. Benkert P, et al. QMEAN server for protein model quality estimation. Nucleic Acids Res. 2009a;37:W510–W514. - PMC - PubMed
    1. Benkert P, et al. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins. 2009b;77(Suppl. 9):173–180. - PubMed
    1. Berman H, et al. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 2003;10:980. - PubMed

Publication types