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MC-DEPI

Monte-Carlo Diffusion-Enhanced Photon Inference (MC-DEPI) is a method to simulate solution-based single-molecule FRET experiments and to estimate physical parameters to the experimental data.

The method is described in:

Monte-Carlo Diffusion-Enhanced Photon Inference: Distance Distributions and Conformational Dynamics in single-molecule FRET

Antonino Ingargiola, Shimon Weiss, Eitan Lerner (2018) https://doi.org/10.1101/385252

The input is the burst-selected photon data from a smFRET experiment. DEPI simulates photon color and nanotimes, based on donor-acceptor self-diffusion. This allows to accurately simulate smFRET experiment taking into account the FRET-enhancenment due to the donor-acceptor diffusion happening during the fluorescence lifetime.

Notebooks

Example notebooks illustrating how to use this package are available here:

Installation

The most update version of depi can be installed from github:

pip install git+https://github.com/OpenSMFS/depi/ --upgrade

Dependencies

  • python >=3.6
  • numpy >=1.9
  • scipy >=1.0
  • matplotlib >=2.0
  • cython >= 0.23
  • pandas >= 0.22
  • joblib >= 0.11