Python Structural DNA helical parameters tutorial
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Download RO-CrateStructural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb)
Based on the NAFlex server and in particular in its Nucleic Acids Analysis section.
This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Drew Dickerson Dodecamer sequence -CGCGAATTCGCG- (PDB code 1BNA). The trajectory used is a 500ns-long MD simulation taken from the BigNASim database (NAFlex_DDD_II entry).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2025 Barcelona Supercomputing Center
- (c) 2015-2025 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version History
Version 5 (latest) Created 6th Aug 2025 at 14:59 by Genís Bayarri
Update to 5.1.*
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Version 4 Created 26th Jul 2023 at 16:48 by Genís Bayarri
Added .curvesplus folder
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Version-4
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Version 3 Created 14th Apr 2023 at 09:48 by Genís Bayarri
Update to BioBB 4.0.*
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Version-3
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Version 2 Created 22nd Nov 2022 at 10:14 by Genís Bayarri
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Version 1 (earliest) Created 17th Mar 2022 at 11:10 by Genís Bayarri
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Views: 6048 Downloads: 2371
Created: 17th Mar 2022 at 11:10
Last updated: 6th Aug 2025 at 15:02
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
