ArticleMolecular simulation
Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.
Article in Molecular simulation. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 168 citations in OpenAlex.
- Article
- Enhanced Sampling and Free Energy Calculations in Protein Simulations.Advances in experimental medicine and biology · 2026Review
- Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions.Journal of chemical theory and computation · 2025Article
- Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions.bioRxiv : the preprint server for biology · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering.Journal of chemical theory and computation · 2024Article
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Accelerating Molecular Dynamics Simulations for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.Journal of chemical information and modeling · 2023Article
- Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems.Journal of chemical information and modeling · 2023Article
- Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes.International journal of molecular sciences · 2023Article
- Application of Molecular Dynamics Simulations to Determine Interactions between Canary Seed (International journal of molecular sciences · 2023Article
- Nitazoxanide Inhibits the Bifunctional Enzyme GlG6PD::6PGL ofInternational journal of molecular sciences · 2023Article
- A New Approach for Estimating the Free Energy Differences among Multiple Thermodynamic States in Statistical Simulations.The journal of physical chemistry letters · 2023Article
- Deep Boosted Molecular Dynamics: Accelerating Molecular Simulations with Gaussian Boost Potentials Generated Using Probabilistic Bayesian Deep Neural Network.The journal of physical chemistry letters · 2023Article
- Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network.bioRxiv : the preprint server for biology · 2023Article
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.The journal of physical chemistry. A · 2022Article
10 more citing papers are in PubMed but not listed here.
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2 authors at 2 institutions in 1 country.
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Abstract
Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.
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