Analysis of DNA hairpin dynamics with FRETraj

Note

Please cite: Fabio D Steffen, Roland K O Sigel, Richard Börner, FRETraj: integrating single-molecule spectroscopy with molecular dynamics, Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3953–3955, https://doi.org/10.1093/bioinformatics/btab615

This repository demonstrates the use of FRETraj for high throughput accessible-contact volume calculation (multi-ACV) and subsequent FRET prediction. The workflow is outlined in an interactive Jupyter notebook which can be run locally or directly on without any installation.

Note: Binder needs to build the image from the repository which can take a few seconds.

We have run an 1 μs MD simulation of a DNA hairpin, computed multi-ACVs for Cy3 and Cy5 at residues T20 and C44 along the trajectory and predicted FRET efficiencies for every snapshot with a timestep of 100 ps.

The repository contains the PBC-corrected MD trajectory (data/DNA_hairpin.xtc), the experimental burst size distribution (data/burst_sizes.dat), the computed and serialized FRET object (data/FRET_DNA_hairpin.pkl) as well as the ACV distances (R_DAsub>, data/R_kappa.dat).