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

scientific article

FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET is …
instance of (P31):
scholarly articleQ13442814

External links are
P819ADS bibcode2016PLoSO..1160716I
P356DOI10.1371/JOURNAL.PONE.0160716
P3181OpenCitations bibliographic resource ID4046187
P932PMC publication ID4988647
P698PubMed publication ID27532626

P50authorSangYoon ChungQ37384141
Antonino IngargiolaQ37384161
Eitan LernerQ37384179
Xavier MichaletQ42562500
P2093author name stringShimon Weiss
P2860cites workA Quick Introduction to Version Control with Git and GitHubQ22341585
Best practices for scientific computingQ24273451
Ten simple rules for the open development of scientific softwareQ24494742
A new look at the statistical model identificationQ26778401
The case for open computer programsQ27921796
Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence ExperimentsQ28602080
Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule dataQ28731931
Interactive notebooks: Sharing the codeQ28851715
Estimating the Dimension of a ModelQ29542197
Shot-noise limited single-molecule FRET histograms: comparison between theory and experimentsQ30499969
A practical guide to single-molecule FRETQ30544576
BOBA FRET: bootstrap-based analysis of single-molecule FRET dataQ30725593
Single-molecule FRET with diffusion and conformational dynamicsQ30834975
Alternating-laser excitation of single moleculesQ30995143
Theory of photon statistics in single-molecule Förster resonance energy transferQ31139781
Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitationQ31141763
Fluorescence spectroscopy of single biomolecules.Q31221311
Data registration and selective single-molecule analysis using multi-parameter fluorescence detectionQ31882181
Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single moleculesQ33203383
Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteinsQ33227189
Concentration effects in "single-molecule" spectroscopyQ33312058
Probing biomolecular structures and dynamics of single molecules using in-gel alternating-laser excitationQ33513264
Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET dataQ33518206
Toward standard practices for sharing computer code and programs in neuroscience.Q46320906
No more hidden solutions in bioinformatics.Q50911011
Characterizing single-molecule FRET dynamics with probability distribution analysis.Q54383789
Towards standard practices for sharing computer code and programs in neuroscienceQ57264878
Computational science: ...ErrorQ59088849
Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds†Q59332561
Measuring conformational dynamics: a new FCS-FRET approachQ80425694
Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transferQ80739537
Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysisQ83001617
On the origin of broadening of single-molecule FRET efficiency distributions beyond shot noise limitsQ84071192
Accurate single-molecule FRET studies using multiparameter fluorescence detectionQ84565031
Decoding the pattern of photon colors in single-molecule FRET.Q33573051
Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP).Q33789209
Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule ExperimentsQ33821494
The renaissance of fluorescence resonance energy transferQ34019505
Disentangling subpopulations in single-molecule FRET and ALEX experiments with photon distribution analysis.Q34190212
Development of new photon-counting detectors for single-molecule fluorescence microscopyQ34319626
FRET efficiency distributions of multistate single moleculesQ34336575
Analysis of single-molecule FRET trajectories using hidden Markov modelingQ34536849
Protein folding studied by single-molecule FRET.Q34742014
Alternating-laser excitation: single-molecule FRET and beyondQ34987528
8-spot smFRET analysis using two 8-pixel SPAD arraysQ35081266
Correlation spectroscopy of minor fluorescent species: signal purification and distribution analysisQ35774452
Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy.Q35872871
Classic maximum entropy recovery of the average joint distribution of apparent FRET efficiency and fluorescence photons for single-molecule burst measurementsQ35873785
Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET MeasurementsQ35877339
Rampant software errors may undermine scientific resultsQ36238101
Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulationsQ36448640
Conformational transitions monitored for single molecules in solutionQ36806187
The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selectionQ37199626
Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experimentsQ37701058
How, when and why proteins collapse: the relation to foldingQ37959224
Kinetics of fast changing intramolecular distance distributions obtained by combined analysis of FRET efficiency kinetics and time-resolved FRET equilibrium measurementsQ42005307
Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis.Q42011250
Pulsed interleaved excitationQ42251940
Photon-by-photon determination of emission bursts from diffusing single chromophoresQ43717186
Detailed study of DNA hairpin dynamics using single-molecule fluorescence assisted by DNA origami.Q44520375
Bayesian inference of accurate population sizes and FRET efficiencies from single diffusing biomoleculesQ44547800
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesJupyter notebook fileQ70357595
P433issue8
P407language of work or nameEnglishQ1860
P921main subjectopen-source softwareQ1130645
P304page(s)e0160716
P577publication date2016-08-17
P1433published inPLOS OneQ564954
P1476titleFRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET
P478volume11

Reverse relations

cites work (P2860)
Q3639877016-Ch Time-resolved Single-Molecule Spectroscopy Using Line Excitation.
Q5639508348-spot single-molecule FRET setup with periodic acceptor excitation
Q46204924A protean clamp guides membrane targeting of tail-anchored proteins.
Q42291744Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments.
Q52335730Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example.
Q64944932ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data.
Q46050828Different types of pausing modes during transcription initiation.
Q55513394Dynamic action of the Sec machinery during initiation, protein translocation and termination.
Q92253698High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins
Q94483980Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients
Q36349749Multispot single-molecule FRET: High-throughput analysis of freely diffusing molecules
Q62104763Multispot single-molecule FRET: high-throughput analysis of freely diffusing molecules
Q88330840PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data
Q33821494Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments
Q55368890Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1.
Q92130068Systematic Assessment of Burst Impurity in Confocal-Based Single-Molecule Fluorescence Detection Using Brownian Motion Simulations
Q101409855The smfBox is an open-source platform for single-molecule FRET
Q47724775Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer.

Search more.