Workflow Type: Jupyter
Stable

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).


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).

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

Version History

Version 2 (latest) 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
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2022). Jupyter Notebook Structural DNA helical parameters tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.195.2
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Views: 865

Created: 28th Sep 2021 at 09:43

Last updated: 17th Mar 2022 at 11:06

Last used: 6th Oct 2022 at 07:53

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