FRETraj

FRETraj predicts FRET efficiencies for single-molecule Förster Resonance Energy Transfer (smFRET) experiments by modeling donor and acceptor dye dynamics using accessible-contact volumes (ACV) to relate transfer efficiencies to atom-to-atom distances in biomolecules.

Key Features:

• Accessible-Contact Volumes (ACV): Computes multiple ACVs along molecular dynamics trajectories to estimate spatial distributions of donor and acceptor dye positions.
• Photon Statistics Simulation: Simulates photon statistics to refine and quantify predicted FRET efficiency distributions.
• Fluorophore Positioning Assessment: Rapidly evaluates donor–acceptor distance distributions to support selection of fluorophore labeling sites.

Scientific Applications:

• Structural Ensemble Analysis: Maps FRET efficiencies to conformational ensembles of dynamic non-coding RNAs and transient protein–nucleic acid complexes by computing ACVs along MD trajectories.
• smFRET Distance Interpretation: Facilitates interpretation of experimental FRET distributions in biomolecular systems, including DNA hairpins, by relating efficiencies to atomistic distances.

Methodology:

Computes multiple ACVs from molecular dynamics simulations, models donor and acceptor dye dynamics to obtain donor–acceptor distance distributions, incorporates simulated photon statistics to generate predicted FRET distributions, and compares predicted distributions with single-molecule experimental data (e.g., DNA hairpins) for validation.