Structural 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.

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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).

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Settings

Biobb module used

• biobb_dna: Tools to analyse DNA structures and MD trajectories.

Auxiliary libraries used

• jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
• matplotlib: Comprehensive library for creating static, animated, and interactive visualizations in Python.

Conda Installation & Launch

git clone https://github.com/bioexcel/biobb_wf_dna_helparms.git
cd biobb_wf_dna_helparms
conda env create -f conda_env/environment.yml
conda activate biobb_dna_helparms_tutorial
jupyter-notebook biobb_wf_dna_helparms/notebooks/biobb_dna_helparms_tutorial.ipynb

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Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder

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Version

2024.1 Release

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) 2015-2024 Barcelona Supercomputing Center
• (c) 2015-2024 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.