Jupyter Notebook Structural DNA helical parameters tutorial
View on GitHub
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 6 (latest) Created 6th Aug 2025 at 14:56 by Genís Bayarri
Update to 5.1.*
Frozen
Version-6fd4aabc
Version 4 Created 26th Jul 2023 at 14:28 by Genís Bayarri
Fixed importlib_metadata bug
Frozen
Version-4
b33c880
Version 3 Created 14th Apr 2023 at 09:45 by Genís Bayarri
Update to BioBB 4.0.*
Frozen
Version-3
7a42ed4
Version 2 Created 15th Sep 2022 at 13:36 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit f7f9ced
Frozen
Version-2
902f865
Version 1 (earliest) Created 28th Sep 2021 at 09:43 by Genís Bayarri
Initial Commit.Taken from Git commit a0fb606
Frozen
Version-1
80da9d4
Creators and Submitter
Views: 7874 Downloads: 2965
Created: 28th Sep 2021 at 09:43
Last updated: 6th Aug 2025 at 14:57
TagsThis item has not yet been tagged.
AttributionsNone
Collections
Interactive Jupyter...
Related items
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/
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
