Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb)
Version 1

Workflow Type: Jupyter
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Summary

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 (NAFlexDDDII entry).

Parameters

Inputs

Parameters needed to configure the workflow:

  • seq: Sequence of the DNA structure (e.g. CGCGAATTCGCG)

  • seq_comp: Complementary sequence of the given DNA structure (e.g. CGCGAATTCGCG)

  • traj: Trajectory for a 500ns Drew Dickerson Dodecamer MD simulation (taken from BigNASim)

  • top: Associated topology for the MD trajectory

help Creators and Submitter
Citation
Bayarri, G., & Hospital, A. (2021). Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.195.1
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Views: 74   Downloads: 2

Created: 28th Sep 2021 at 09:43

Last used: 17th Oct 2021 at 05:01

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Version 1 Created 28th Sep 2021 at 09:43 by Genís Bayarri

Initial Commit.Taken from Git commit a0fb606

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