# Research Object Crate for Jupyter Notebook Structural DNA helical parameters tutorial

Original URL: https://workflowhub.eu/workflows/195/ro_crate?version=4

# Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb) **Based on the [NAFlex](https://mmb.irbbarcelona.org/NAFlex) server and in particular in its [Nucleic Acids Analysis section](https://mmb.irbbarcelona.org/NAFlex/help.php?id=tutorialAnalysisNA).** *** 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](https://www.rcsb.org/structure/1BNA)). The trajectory used is a 500ns-long MD simulation taken from the [BigNASim](https://mmb.irbbarcelona.org/BIGNASim/) database ([NAFlex_DDD_II](https://mmb.irbbarcelona.org/BIGNASim/getStruc.php?idCode=NAFlex_DDD_II) entry). *** ## Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")

Author
  Adam Hospital, Genís Bayarri
License
  Apache-2.0

## Contents

Main Workflow: Jupyter Notebook Structural DNA helical parameters tutorial
Size: 74219 bytes
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/master/biobb_wf_dna_helparms/notebooks/TRAJ/structure.stripped.nc
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/master/biobb_wf_dna_helparms/notebooks/TRAJ/structure.stripped.top
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/master/conda_env/environment.yml
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/master/.curvesplus/standard_b.lib
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/master/.curvesplus/standard_i.lib
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/master/.curvesplus/standard_s.lib