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openstructure

Description

openstructure website

Open-Source Computational Structural Biology Framework

Environment Modules

Run module spider openstructure to find out what environment modules are available for this application.

Environment Variables

  • HPC_OPENSTRUCTURE_DIR - installation directory

Additional Usage Information

Included Commands: 

OST (or ost) - OpenStructure binary

lDDT (or lddt) - The Local Distance Difference Test

Molck (or molck) - Molecular checker

ChemdictTool (or chemdict_tool) - Creating or update a compound library

tmalign

tmscore

Citation

If you publish research that uses openstructure you have to cite it as follows:

  • Biasini, M., Schmidt, T., Bienert, S., Mariani, V., Studer, G., Haas, J., Johner, N., Schenk, A. D., Philippsen, A., & Schwede, T. (2013). OpenStructure: an integrated software framework for computational structural biology. Acta Crystallographica Section D: Biological Crystallography. https://doi.org/10.1107/S0907444913007051
  • Mariani, V., Biasini, M., Barbato, A., & Schwede, T. (2013). lDDT: A local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics, 29(21), 2722–2728. https://doi.org/10.1093/bioinformatics/btt473

If you use the code in OpenStructure to compute QS scores, please also cite the following reference:

  • Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7, 10480. https://doi.org/10.1038/s41598-017-09654-8

Categories

biology