ArticleNature methods2012
A toolkit and benchmark study for FRET-restrained high-precision structural modeling.
Article in Nature methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 228 papers.
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228 citing papers in PubMed.
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- Identification of 14-3-3 Proteins as Binding Partners of TRP Channels.Journal of chemical information and modeling · 2026Article
- FAMP: A Software Framework for FRET-Based Integrative Modeling of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Cryogenic light microscopy of vitrified samples with angstrom precision.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- 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
- Time-Resolved Fluorescence Detection of Nicked DNA via Site-Specific Stacking of Sulfo-Cy3: The Role of Charge, Polarity, Linker, and Sequence Context.The journal of physical chemistry. B · 2025Article
- The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent.Nucleic acids research · 2025Article
- The functional dynamics of FicD's TPR domain are modulated by the interaction with ATP and BiP.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics.Proteins · 2025Review
- A chemoreceptor conformational equilibrium controlled by signaling inputs.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mechanism of human α3β GlyR regulation by intracellular M3/M4 loop phosphorylation and 2,6-di-tert-butylphenol interaction.Nature communications · 2025Article
- Labelizer: systematic selection of protein residues for covalent fluorophore labeling.Nature communications · 2025Article
- Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules.Journal of visualized experiments : JoVE · 2025Article
- Mechanistic insights into the activity of SARS-CoV-2 RNA polymerase inhibitors using single-molecule FRET.Nucleic acids research · 2025Article
168 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a comprehensive toolkit for Förster resonance energy transfer (FRET)-restrained modeling of biomolecules and their complexes for quantitative applications in structural biology. A dramatic improvement in the precision of FRET-derived structures is achieved by explicitly considering spatial distributions of dye positions, which greatly reduces uncertainties due to flexible dye linkers. The precision and confidence levels of the models are calculated by rigorous error estimation. The accuracy of this approach is demonstrated by docking a DNA primer-template to HIV-1 reverse transcriptase. The derived model agrees with the known X-ray structure with an r.m.s. deviation of 0.5 Å. Furthermore, we introduce FRET-guided 'screening' of a large structural ensemble created by molecular dynamics simulations. We used this hybrid approach to determine the formerly unknown configuration of the flexible single-strand template overhang.
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