ArticleNature communications2022
A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- An integrated open-source acquisition and analysis ecosystem for high-throughput single-molecule imaging.Nature methods · 2026Article
- Benchmarking dynamic analysis methods in diffusion-based single-molecule FRET.Cell reports methods · 2026Article
- Automated kinetic-scheme-free sorting of single-molecule fluorescence events using a deep learning based hidden-state method.Nature communications · 2026Article
- Denoise Stepwise Signals by Diffusion Model-Based Approach.Small methods · 2026Article
- Graph neural network modeling of receptor interaction kinetics from single-molecule imaging data.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule FRET and tracking of transfected biomolecules in living cells.Biophysical journal · 2026Article
- A Standardized Prism-Based TIRF Platform for Quantitative Single-Molecule Fluorescence Studies of Biomolecular Dynamics.Biosensors · 2026Article
- Advancements in single-molecule fluorescence spectroscopy for probing conformations, dynamics, and interactions in disordered protein regions.Current opinion in structural biology · 2026Review
- Multiplexed single-molecule characterization at the library scale.Nature protocols · 2026Review
- Single-molecule parallel analysis for rapid exploration of sequence space.Nature protocols · 2026Review
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- A cautious user's guide in applying HMMs to physical systems.The Journal of chemical physics · 2025Article
- FRET-FCS: Advancing comprehensive insights into complex biological systems.Biophysical journal · 2025Review
- Review
- Foundation model for efficient biological discovery in single-molecule time traces.Nature methods · 2025Article
- Quantum relaxometry for detecting biomolecular interactions with single NV centers.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Bayesian Nonparametrics for FRET using Realistic Integrative Detectors.bioRxiv : the preprint server for biology · 2025Article
- Single-molecule reaction-diffusion.Biophysical journal · 2025Article
- Article
- Pretrained Deep Neural Network Kin-SiM for Single-Molecule FRET Trace Idealization.The journal of physical chemistry. B · 2025Article
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29 authors.
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Abstract
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We test them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise levels, varied model complexity, non-equilibrium dynamics, and kinetic heterogeneity. Our results highlight the current strengths and limitations in inferring kinetic information from smFRET trajectories. In addition, we formulate concrete recommendations and identify key targets for future developments, aimed to advance our understanding of biomolecular dynamics through quantitative experiment-derived models.
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