ArticleBioinformatics (Oxford, England)2021
FRETraj: integrating single-molecule spectroscopy with molecular dynamics.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Capping protein dynamics are defined by the stalk and restricted by CPI-motif and V-1 binding.Biophysical journal · 2026Article
- A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.Scientific reports · 2026Article
- FRET-guided selection of RNA 3D structures.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 dimerization domain of SARS-CoV-2 nucleocapsid protein is partially disordered and forms a dynamic high-affinity dimer.Cell reports. Physical science · 2025Article
- Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.Nanoscale · 2025Article
- FRET-guided modeling of nucleic acids.Nucleic acids research · 2024Article
- FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries.Communications biology · 2024Article
- Biophysical Mechanism of Allosteric Regulation of Actin Capping Protein.Journal of molecular biology · 2023Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
- Article
- Coevolution and smFRET Enhances Conformation Sampling and FRET Experimental Design in Tandem PDZ1-2 Proteins.The journal of physical chemistry. B · 2023Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
summaryQuantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact volumes (ACV) and simulated photon statistics. FRETraj helps to identify optimal fluorophore positions on a biomolecule of interest by rapidly evaluating donor-acceptor distances. FRETraj is scalable and fully integrated into PyMOL and the Jupyter ecosystem. Here, we describe the conformational dynamics of a DNA hairpin by computing multiple ACVs along a molecular dynamics trajectory and compare the predicted FRET distribution with single-molecule experiments. FRET-assisted modeling will accelerate the analysis of structural ensembles in particular dynamic, non-coding RNAs and transient protein-nucleic acid complexes. AVAILABILITY AND IMPLEMENTATION: FRETraj is implemented as a cross-platform Python package available under the GPL-3.0 on Github (https://github.com/RNA-FRETools/fretraj) and is documented at https://RNA-FRETools.github.io/fretraj. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.