ArticleJournal of chemical theory and computation2015
Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.
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. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.Journal of chemical theory and computation · 2023Article
- How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2.RSC advances · 2023Article
- Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields.Physical chemistry chemical physics : PCCP · 2023Article
- ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.Journal of chemical theory and computation · 2023Article
- CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.Protein science : a publication of the Protein Society · 2022Article
- Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids.The journal of physical chemistry. B · 2021Article
- Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review.Journal of chemical information and modeling · 2021Review
- Insights into substrate recognition and specificity for IgG by Endoglycosidase S2.PLoS computational biology · 2021Article
- Site-Selective Chemoenzymatic Modification on the Core Fucose of an Antibody Enhances Its Fcγ Receptor Affinity and ADCC Activity.Journal of the American Chemical Society · 2021Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.Journal of chemical theory and computation · 2020Article
- Long-range Regulation of Partially Folded Amyloidogenic Peptides.Scientific reports · 2020Article
- Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design.Carbohydrate research · 2019Article
- Article
- Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes.Journal of chemical information and modeling · 2017Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
- CHARMM-GUI 10 years for biomolecular modeling and simulation.Journal of computational chemistry · 2017Review
- Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4.The journal of physical chemistry. B · 2017Article
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3 authors.
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Abstract
Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems.
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