ArticleProceedings of the National Academy of Sciences of the United States of America2011
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Building multiscale Markov state models by systematic mapping of temporal communities.Bioinformatics (Oxford, England) · 2026Article
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders.The Journal of chemical physics · 2021Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide.The journal of physical chemistry. B · 2021Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Heterogeneity in the Folding of Villin Headpiece Subdomain HP36.The journal of physical chemistry. B · 2018Article
- SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes.Scientific reports · 2018Article
- Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.Nature communications · 2017Article
- Optimized parameter selection reveals trends in Markov state models for protein folding.The Journal of chemical physics · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.Protein science : a publication of the Protein Society · 2016Article
- Markov state models of protein misfolding.The Journal of chemical physics · 2016Article
- The unusual internal motion of the villin headpiece subdomain.Protein science : a publication of the Protein Society · 2016Article
- Accelerated molecular dynamics simulations of protein folding.Journal of computational chemistry · 2015Article
- A network of molecular switches controls the activation of the two-component response regulator NtrC.Nature communications · 2015Article
- A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain.Biophysical journal · 2015Article
- High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.Journal of chemical theory and computation · 2013Article
- Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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Authors and funding
4 authors.
Funding
Abstract
As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of molecular dynamics and Markov state models, we connect to current experimental results in three ways. First, we present and validate a novel method for the quantitative prediction of triplet-triplet energy transfer experiments. Second, we construct a many-state model for HP35 that is consistent with previous experiments. Finally, we predict contact-formation time traces for all 1,225 possible triplet-triplet energy transfer experiments on HP35.
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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.