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oxDNA_duplex_analysis

Take a look at the following papers for an idea of what kinds of things can be done with oxDNA:

  1. Original oxDNA paper
  2. oxDNA analysis tools
  3. Hairpins
  4. A review of feature extraction from molecular simulations

Clone oxDNA from the Github, follow the instructions in the installation section of the documentation (with Python bindings enabled and CUDA enabled if you have a GPU). I would suggest trying the OXPY_Jupyter example

Feature_Analysis

Notebook for feature analysis of oxDNA simulation results.

  1. The Google Colaboratory first installs oxDNA & oxDNA Analysis tools, then loads up trajectory, topology, and input file of the sequence in the mounted google drive directory, and generates nucleotide pairs through a modification of duplex_finder.py

  2. The features obtained from the simulation results are: Sequence Length, Average of % dsDNA, Average of % ssDNA, Standard Deviation % dsDNA, Standard Deviation % ssDNA, # of dsDNA fragments, Standard Deviation of # dsDNA fragments, Relative Percentage Abundance of dsDNA/Sequence Length.

  3. The nucleotide pairs are transformed into a dataframe, and features are calculated for the given sequence simulation, alongwith recording the time for generating the pairs, and for pair analysis.