ArticleJournal of chemical theory and computation2015
Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A.bioRxiv : the preprint server for biology · 2025Article
- Shaping the Glycan Landscape: Hidden Relationships between Linkage and Ring Distortions Induced by Carbohydrate-Active Enzymes.Journal of the American Chemical Society · 2025Article
- Unbiased Enhanced Sampling in Molecular Dynamics via Simultaneously Accelerating Diffusion in Multiple Low-Dimensional Collective Variable Spaces.Journal of chemical theory and computation · 2025Article
- How chromatin-binding proteins direct distinct folding pathways of tetra-nucleosomes: Insights from coarse-grained simulations.bioRxiv : the preprint server for biology · 2025Article
- Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA.Nucleic acids research · 2025Article
- Opportunities and challenges in modelling ligand adsorption on semiconductor nanocrystals.Communications chemistry · 2025Review
- Structural bioinformatics for rational drug design.Research and practice in thrombosis and haemostasis · 2025Article
- Absolute Binding Free Energies with OneOPES.The journal of physical chemistry letters · 2024Article
- OneOPES, a Combined Enhanced Sampling Method to Rule Them All.Journal of chemical theory and computation · 2023Article
- Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions.Journal of chemical theory and computation · 2023Article
- From data to noise to data for mixing physics across temperatures with generative artificial intelligence.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Modeling Adsorption, Conformation, and Orientation of the Fis1 Tail Anchor at the Mitochondrial Outer Membrane.Membranes · 2022Article
- Multiscale modelling of claudin-based assemblies: A magnifying glass for novel structures of biological interfaces.Computational and structural biotechnology journal · 2022Review
- Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling.The journal of physical chemistry. A · 2021Article
- Computational methods for exploring protein conformations.Biochemical Society transactions · 2020Review
- Adapting free energy perturbation simulations for large macrocyclic ligands: how to dissect contributions from direct binding and free ligand flexibility.Chemical science · 2020Article
- Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data.Nucleic acids research · 2020Article
- Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.Journal of chemical information and modeling · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.
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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.