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FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

https://doi.org/10.1101/039198
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Theory of Single‐Molecule FRET Efficiency Histograms
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Characterizing Single‐Molecule FRET Dynamics with Probability Distribution Analysis
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WaveLab and Reproducible Research
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Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data
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Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis
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Disentangling Subpopulations in Single-Molecule FRET and ALEX Experiments with Photon Distribution Analysis
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Kinetics of Fast Changing Intramolecular Distance Distributions Obtained by Combined Analysis of FRET Efficiency Kinetics and Time-Resolved FRET Equilibrium Measurements
inferredcites →https://doi.org/10.1016/j.bpj.2013.12.055openalex-snapshot
Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments
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Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments
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Open source tools for large-scale neuroscience
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The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection
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Publishing scientific software matters
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Protein folding studied by single-molecule FRET
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How, when and why proteins collapse: the relation to folding
inferredcites →https://doi.org/10.1016/s0076-6879(10)75018-7openalex-snapshot
Accurate Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection
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Data registration and selective single-molecule analysis using multi-parameter fluorescence detection
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Ratiometric measurement and identification of single diffusing molecules
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Probing Biomolecular Structures and Dynamics of Single Molecules Using In-gel Alternating-Laser Excitation
inferredcites →https://doi.org/10.1021/ar0401348openalex-snapshot
Alternating-Laser Excitation of Single Molecules
inferredcites →https://doi.org/10.1021/jp0546047openalex-snapshot
Photon-by-Photon Determination of Emission Bursts from Diffusing Single Chromophores
inferredcites →https://doi.org/10.1021/jp057257+openalex-snapshot
Separating Structural Heterogeneities from Stochastic Variations in Fluorescence Resonance Energy Transfer Distributions via Photon Distribution Analysis
inferredcites →https://doi.org/10.1021/jp063483nopenalex-snapshot
Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments
inferredcites →https://doi.org/10.1021/jp070659sopenalex-snapshot
Measuring Conformational Dynamics: A New FCS-FRET Approach
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Probability Distribution Analysis of Single-Molecule Fluorescence Anisotropy and Resonance Energy Transfer
inferredcites →https://doi.org/10.1021/jp075255eopenalex-snapshot
Single-Molecule FRET with Diffusion and Conformational Dynamics
inferredcites →https://doi.org/10.1021/jp0764182openalex-snapshot
Concentration Effects in “Single-Molecule” Spectroscopy
inferredcites →https://doi.org/10.1021/jp076971jopenalex-snapshot
Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds
inferredcites →https://doi.org/10.1021/jp100025vopenalex-snapshot
On the Origin of Broadening of Single-Molecule FRET Efficiency Distributions beyond Shot Noise Limits
inferredcites →https://doi.org/10.1021/jp105359zopenalex-snapshot
FRET Efficiency Distributions of Multistate Single Molecules
inferredcites →https://doi.org/10.1021/jp4059214openalex-snapshot
Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami
inferredcites →https://doi.org/10.1021/jp903671popenalex-snapshot
Decoding the Pattern of Photon Colors in Single-Molecule FRET
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Quantitative Identification of Different Single Molecules by Selective Time-Resolved Confocal Fluorescence Spectroscopy
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Computational science: ...Error
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Mozilla plan seeks to debug scientific code
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Interactive notebooks: Sharing the code
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Rule rewrite aims to clean up scientific software
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No more hidden solutions in bioinformatics
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The renaissance of fluorescence resonance energy transfer.
inferredcites →https://doi.org/10.1038/nature10836openalex-snapshot
The case for open computer programs
inferredcites →https://doi.org/10.1038/nmeth.1208openalex-snapshot
A practical guide to single-molecule FRET
inferredcites →https://doi.org/10.1038/nn.4550openalex-snapshot
Toward standard practices for sharing computer code and programs in neuroscience
inferredcites →https://doi.org/10.1039/c0cp01911aopenalex-snapshot
Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP)
inferredcites →https://doi.org/10.1039/c3cs60233hopenalex-snapshot
Alternating-laser excitation: single-molecule FRET and beyond
inferredcites →https://doi.org/10.1063/1.1812746openalex-snapshot
Theory of photon statistics in single-molecule Förster resonance energy transfer
inferredcites →https://doi.org/10.1063/1.3230974openalex-snapshot
Förster transfer outside the weak-excitation limit
inferredcites →https://doi.org/10.1073/pnas.0401690101openalex-snapshot
Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules
inferredcites →https://doi.org/10.1073/pnas.0508584102openalex-snapshot
Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins
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Conformational transitions monitored for single molecules in solution.
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Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy
inferredcites →https://doi.org/10.1073/pnas.96.7.3670openalex-snapshot
Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Förster distance dependence and subpopulations
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EDF Statistics for Goodness of Fit and Some Comparisons
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Minimum Distance and Robust Estimation
inferredcites →https://doi.org/10.1098/rstb.2012.0035openalex-snapshot
Development of new photon-counting detectors for single-molecule fluorescence microscopy
inferredcites →https://doi.org/10.1109/tac.1974.1100705openalex-snapshot
A new look at the statistical model identification
inferredcites →https://doi.org/10.1111/j.1467-9876.2005.00509.xopenalex-snapshot
Bayesian Analysis of Single-Molecule Experimental Data
inferredcites →https://doi.org/10.1117/12.2003704openalex-snapshot
8-spot smFRET analysis using two 8-pixel SPAD arrays
inferredcites →https://doi.org/10.1117/12.2212085openalex-snapshot
Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments
inferredcites →https://doi.org/10.1126/science.1131399openalex-snapshot
Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
inferredcites →https://doi.org/10.1126/science.283.5408.1676openalex-snapshot
Fluorescence Spectroscopy of Single Biomolecules
inferredcites →https://doi.org/10.1214/aos/1176344136openalex-snapshot
Estimating the Dimension of a Model
inferredcites →https://doi.org/10.12688/f1000research.5930.2openalex-snapshot
Rampant software errors may undermine scientific results
inferredcites →https://doi.org/10.1371/journal.pbio.1001745openalex-snapshot
Best Practices for Scientific Computing
inferredcites →https://doi.org/10.1371/journal.pcbi.1002802openalex-snapshot
Ten Simple Rules for the Open Development of Scientific Software
inferredcites →https://doi.org/10.1371/journal.pcbi.1004668openalex-snapshot
A Quick Introduction to Version Control with Git and GitHub
inferredcites →https://doi.org/10.1371/journal.pone.0030024openalex-snapshot
Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data
inferredcites →https://doi.org/10.1371/journal.pone.0084157openalex-snapshot
BOBA FRET: Bootstrap-Based Analysis of Single-Molecule FRET Data
inferredcites →https://doi.org/10.1371/journal.pone.0143732openalex-snapshot
Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements
inferredcites →https://doi.org/10.1529/biophysj.104.054114openalex-snapshot
Accurate FRET Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation
inferredcites →https://doi.org/10.1529/biophysj.105.064766openalex-snapshot
Pulsed Interleaved Excitation
inferredcites →https://doi.org/10.1529/biophysj.106.082487openalex-snapshot
Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling
inferredcites →https://doi.org/10.1529/biophysj.106.093591openalex-snapshot
Correlation Spectroscopy of Minor Fluorescent Species: Signal Purification and Distribution Analysis
inferredcites →https://doi.org/10.17863/cam.7376openalex-snapshot
pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis
inferredcites →https://doi.org/10.5281/zenodo.592536openalex-snapshot
Matplotlib version 1.4.0
inferredcites →https://doi.org/10.5281/zenodo.592845openalex-snapshot
mwaskom/seaborn v0.11.0.rc0
inferredcites →https://doi.org/10.5281/zenodo.598352openalex-snapshot
LMFIT: Non-Linear Least-Square Minimization and Curve-Fitting for Python

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2022.08.03.502619openalex-snapshot
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins
inferred← citeshttps://doi.org/10.1101/2025.07.17.665365openalex-snapshot
A protein-dependent riboswitch activates ribosomal frameshifting in cardioviruses
inferred← citeshttps://doi.org/10.1117/12.2212085openalex-snapshot
Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments
inferred← citeshttps://doi.org/10.1117/12.2608487openalex-snapshot
A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format
inferred← citeshttps://doi.org/10.1371/journal.pone.0143732openalex-snapshot
Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements
inferred← citeshttps://doi.org/10.3390/cells11162475openalex-snapshot
N-Terminal Tails of Histones H2A and H2B Differentially Affect Transcription by RNA Polymerase II In Vitro
inferred← citeshttps://doi.org/10.3390/ijms242015194openalex-snapshot
Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study
inferred← citeshttps://doi.org/10.3390/molecules24142557openalex-snapshot
Systematic Assessment of Burst Impurity in Confocal-Based Single-Molecule Fluorescence Detection Using Brownian Motion Simulations
inferred← citeshttps://doi.org/10.3791/62378openalex-snapshot
Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox
inferred← citeshttps://doi.org/10.3791/62378-vopenalex-snapshot
Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox
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