ArticlePloS one2016
FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- DNA damage induces long range changes to duplex structure-a non-protein start to damage detection?Nucleic acids research · 2026Article
- Benchmarking dynamic analysis methods in diffusion-based single-molecule FRET.Cell reports methods · 2026Article
- GTPase cycle and ER membrane regulate cargo handover during cotranslational protein targeting.Science advances · 2026Article
- Dissecting mechanisms of ligand binding and conformational changes in the glutamine-binding protein.eLife · 2026Article
- BLeaching In-cell Single-molecule burstS (BLISS) reveals a small dynamic fraction of HP1α clusters in undifferentiated embryonic stem cells.bioRxiv : the preprint server for biology · 2026Article
- Electronic Actuation of Surface-Immobilized, pH-Responsive DNA Nanoswitches.ACS applied materials & interfaces · 2026Article
- Kinesin-1 is highly flexible and adopts an open conformation in the absence of cargo.iScience · 2026Article
- Delineation of a novel assembly intermediate in Rous sarcoma virus integration pathway.Nucleic acids research · 2026Article
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states.Nucleic acids research · 2026Article
- Cryo-EM structure of influenza polymerase bound to the cRNA promoter provides insights into the mechanism of viral replication.Communications biology · 2025Article
- A DNA Scaffold Approach Facilitates 5' Labeling of the SARS-CoV-2 RNA Pseudoknot for Single-Molecule Förster Resonance Energy Transfer Investigation.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Global conformation of the Rag GTPase heterodimer governs eukaryotic amino acid sensing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Quantitative analysis methods for free diffusion single-molecule FRET experiments.Current opinion in structural biology · 2025Review
- Single-molecule reaction-diffusion.Biophysical journal · 2025Article
- Single-molecule visualization of ATP-induced dynamics of the subunit composition of an ECF transporter complex under turnover conditions.Nature communications · 2025Article
- Mechanistic insights into the activity of SARS-CoV-2 RNA polymerase inhibitors using single-molecule FRET.Nucleic acids research · 2025Article
- tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.Bioinformatics (Oxford, England) · 2025Article
- RNA helicases DDX3X and DDX3Y form nanometer-scale RNA-protein clusters that support catalytic activity.Current biology : CB · 2024Article
- Specific catalytically impaired DDX3X mutants form sexually dimorphic hollow condensates.Nature communications · 2024Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community.
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