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:

• https://github.com/tritemio/mcdepi2018-paper-analysis

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