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.
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).
- biobb_dna: Tools to analyse DNA structures and MD trajectories.
- 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.
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_wf_dna_helparms
jupyter-notebook biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynbClick here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
Click here to open tutorial in Google Colab
2024.1 Release
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.
