ArticleBiophysical journal2010
Linking well-tempered metadynamics simulations with experiments.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
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- Gaussian Process Regression for Mapping Free EnergyLandscape of MgMolecules (Basel, Switzerland) · 2025Article
- Estimation of vibrational spectra of Trp-cage protein from nonequilibrium metadynamics simulations.Biophysical journal · 2024Article
- Molecular View on theJournal of chemical information and modeling · 2023Article
- Structural Characterization of Nanobodies during Germline Maturation.Biomolecules · 2023Article
- Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Review
- Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations.Journal of chemical theory and computation · 2022Article
- The influence of antibody humanization on shark variable domain (VNAR) binding site ensembles.Frontiers in immunology · 2022Article
- Structural Determinants of Substrate Recognition and Catalysis by Heparan Sulfate Sulfotransferases.ACS catalysis · 2021Article
- Shark Antibody Variable Domains Rigidify Upon Affinity Maturation-Understanding the Potential of Shark Immunoglobulins as Therapeutics.Frontiers in molecular biosciences · 2021Article
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
- Free-energy studies reveal a possible mechanism for oxidation-dependent inhibition of MGL.Scientific reports · 2016Article
- The allosteric switching mechanism in bacteriophage MS2.The Journal of chemical physics · 2016Article
- Using Markov state models to study self-assembly.The Journal of chemical physics · 2014Article
- The Parkinson disease-linked LRRK2 protein mutation I2020T stabilizes an active state conformation leading to increased kinase activity.The Journal of biological chemistry · 2014Article
- Free-energy landscape of protein oligomerization from atomistic simulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data.
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