ArticleNature communications2020
Automated and optimally FRET-assisted structural modeling.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Quantitative Integration of FRET and Molecular Dynamics for Modeling Flexible Peptides.The journal of physical chemistry. B · 2026Article
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
- The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states.Nucleic acids research · 2026Article
- FAMP: A Software Framework for FRET-Based Integrative Modeling of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A DNA Scaffold Approach Facilitates 5' Labeling of the SARS-CoV-2 RNA Pseudoknot for Single-Molecule Förster Resonance Energy Transfer Investigation.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Model-free photon analysis of diffusion-based single-molecule FRET experiments.Nature communications · 2025Article
- Labelizer: systematic selection of protein residues for covalent fluorophore labeling.Nature communications · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.Nanoscale · 2025Article
- Multistate kinetics of the syringe-like injection mechanism of Tc toxins.Science advances · 2025Article
- Article
- Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.Protein science : a publication of the Protein Society · 2024Article
- Advanced multiparametric image spectroscopy and super-resolution microscopy reveal a minimal model of CD95 signal initiation.Science advances · 2024Article
- Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.ArXiv · 2024Article
- FRET-guided modeling of nucleic acids.Nucleic acids research · 2024Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
- Article
- Article
- Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET.Methods (San Diego, Calif.) · 2023Article
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Authors and funding
8 authors.
Funding
Abstract
FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity of FRET experiments, they need to be combined with computer simulations. We introduce a program suite with (i) an automated design tool for FRET experiments, which determines how many and which FRET pairs should be used to minimize the uncertainty and maximize the accuracy of an integrative structure, (ii) an efficient approach for FRET-assisted coarse-grained structural modeling, and all-atom molecular dynamics simulations-based refinement, and (iii) a quantitative quality estimate for judging the accuracy of FRET-derived structures as opposed to precision. We benchmark our tools against simulated and experimental data of proteins with multiple conformational states and demonstrate an accuracy of ~3 Å RMSD
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Registered trials
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