ArticleMethods in molecular biology (Clifton, N.J.)2018
Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example.
Article in Methods in molecular biology (Clifton, N.J.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed.
- Replica Exchange Molecular Dynamics with Hydrogen Mass Repartitioning Improves Sampling of Peptide Binding to a Lipid Bilayer.Journal of chemical theory and computation · 2026Article
- Integrating molecular dynamics simulations to enable rational assembly of immune signals for immunotherapy.Nanoscale horizons · 2026Article
- Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide.Journal of chemical information and modeling · 2026Article
- A Theoretical Study of Clorsulon-Imprinted Polypyrrole: Modeling Complementary Cavity Formation and Rebinding of Clorsulon.ACS measurement science au · 2026Article
- Transient Aggregation-Prone States in Disordered Proteins as Therapeutic Targets: The Amyloid-β Case.Journal of chemical information and modeling · 2026Article
- An engineered disulfide staple restricts lid loop dynamics and alters substrate specificity of phenylalanine ammonia-lyase.bioRxiv : the preprint server for biology · 2026Article
- Natural Products in Epilepsy Treatment: From Traditional Medicine Towards Computational Drug Discovery.Current issues in molecular biology · 2026Review
- Article
- Physiological Implications of Pancreatic Amyloid Polypeptide Aggregation and Its Inhibition by Melatonin.International journal of molecular sciences · 2026Review
- Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis.Scientific reports · 2026Article
- Accelerating Replica Exchange Molecular Dynamics: A Comparison of Hydrogen Mass Repartitioning and Light Water Models.Journal of chemical theory and computation · 2026Article
- Lubricin's Mucin Domain Has Strong Polyproline Type II Helical Character.Computational and structural biotechnology journal · 2026Article
- SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations.The journal of physical chemistry. B · 2025Article
- Structural and functional characterization of the Pro64Ser leptin mutant: Implications for congenital leptin deficiency.Biophysical journal · 2025Article
- Molecular dynamics as a tool for unveiling protein-like folding behavior in urethane-based macromolecules: the effect of chain length on the secondary structure of oligourethanes.Polymer chemistry · 2025Article
- Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA.Proteins · 2025Article
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Conformational dynamics of the active state of β-arrestin 1.bioRxiv : the preprint server for biology · 2025Article
- Estimation of Absolute Binding Free Energies for Drugs That Bind Multiple Proteins.Journal of chemical information and modeling · 2025Article
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4 authors.
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Abstract
Protein aggregation is associated with many human diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and type II diabetes (T2D). Understanding the molecular mechanism of protein aggregation is essential for therapy development. Molecular dynamics (MD) simulations have been shown as powerful tools to study protein aggregation. However, conventional MD simulations can hardly sample the whole conformational space of complex protein systems within acceptable simulation time as it can be easily trapped in local minimum-energy states. Many enhanced sampling methods have been developed. Among these, the replica exchange molecular dynamics (REMD) method has gained great popularity. By combining MD simulation with the Monte Carlo algorithm, the REMD method is capable of overcoming high energy-barriers easily and of sampling sufficiently the conformational space of proteins. In this chapter, we present a brief introduction to REMD method and a practical application protocol with a case study of the dimerization of the 11-25 fragment of human islet amyloid polypeptide (hIAPP(11-25)), using the GROMACS software. We also provide solutions to problems that are often encountered in practical use, and provide some useful scripts/commands from our research that can be easily adapted to other systems.
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