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A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories.
Götz, Markus; Barth, Anders; Bohr, Søren S-R; Börner, Richard; Chen, Jixin; Cordes, Thorben; Erie, Dorothy A; Gebhardt, Christian; Hadzic, Mélodie C A S; Hamilton, George L; Hatzakis, Nikos S; Hugel, Thorsten; Kisley, Lydia; Lamb, Don C; de Lannoy, Carlos; Mahn, Chelsea; Dunukara, Dushani; de Ridder, Dick; Sanabria, Hugo; Schimpf, Julia; Seidel, Claus A M; Sigel, Roland K O; Sletfjerding, Magnus Berg; Thomsen, Johannes; Vollmar, Leonie; Wanninger, Simon; Weninger, Keith R; Xu, Pengning; Schmid, Sonja.
Affiliation
  • Götz M; Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, 60 rue de Navacelles, 34090, Montpellier, France. goetz@picoquant.com.
  • Barth A; PicoQuant GmbH, Rudower Chaussee 29, 12489, Berlin, Germany. goetz@picoquant.com.
  • Bohr SS; Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225, Düsseldorf, Germany.
  • Börner R; Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands.
  • Chen J; Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark.
  • Cordes T; Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
  • Erie DA; Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
  • Gebhardt C; Laserinstitut Hochschule Mittweida, University of Applied Sciences Mittweida, 09648, Mittweida, Germany.
  • Hadzic MCAS; Department of Chemistry and Biochemistry, Ohio University, Athens, OH, USA.
  • Hamilton GL; Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.
  • Hatzakis NS; Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA.
  • Hugel T; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
  • Kisley L; Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.
  • Lamb DC; Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
  • de Lannoy C; Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
  • Mahn C; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.
  • Dunukara D; Department of Chemistry & Nano-science Center, University of Copenhagen, 2100, Copenhagen, Denmark.
  • de Ridder D; Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
  • Sanabria H; Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.
  • Schimpf J; Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
  • Seidel CAM; Department of Physics, Case Western Reserve University, Cleveland, OH, USA.
  • Sigel RKO; Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA.
  • Sletfjerding MB; Department of Chemistry and Center for Nano Science (CeNS), Ludwig Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany.
  • Thomsen J; Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
  • Vollmar L; Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA.
  • Wanninger S; Department of Physics, Case Western Reserve University, Cleveland, OH, USA.
  • Weninger KR; Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
  • Xu P; Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
  • Schmid S; Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.
Nat Commun ; 13(1): 5402, 2022 09 14.
Article in En | MEDLINE | ID: mdl-36104339
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Benchmarking / Fluorescence Resonance Energy Transfer Type of study: Clinical_trials Language: En Journal: Nat Commun Journal subject: BIOLOGIA / CIENCIA Year: 2022 Document type: Article Affiliation country: France Country of publication: United kingdom
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Benchmarking / Fluorescence Resonance Energy Transfer Type of study: Clinical_trials Language: En Journal: Nat Commun Journal subject: BIOLOGIA / CIENCIA Year: 2022 Document type: Article Affiliation country: France Country of publication: United kingdom