ArticleAnnual reports in computational chemistry2017
Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.
Article in Annual reports in computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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81 citing papers in PubMed.
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- Molecular determinants of TNFR1:TNFα binding and dynamics in a physiological membrane environment.Current research in structural biology · 2026Article
- Structural basis and physiological significance of non-canonical GNature communications · 2026Article
- E50A Mutation Increases the Bioluminescence Activity of picALuc.Biosensors · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
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- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Investigation of the Substrate Selection Mechanism of Poly (A) Polymerase Based on Molecular Dynamics Simulations and Markov State Model.International journal of molecular sciences · 2025Article
- Gaussian Accelerated Molecular Dynamics Simulations Combined with NRIMD to Explore the Mechanism of Substrate Selectivity of Cid1 Polymerase for Different Nucleoside Triphosphates.International journal of molecular sciences · 2025Article
- The role of hydrophobic collapse in cytotoxic and functional amyloid oligomerization.Biophysical journal · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Mechanistic studies of small molecule ligands selective to RNA single G bulges.Nucleic acids research · 2025Article
- Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.PLoS computational biology · 2025Article
- Mechanisms of Peptide Agonist Dissociation and Deactivation of Adhesion G-Protein-Coupled Receptors.Biochemistry · 2025Article
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- Mechanisms of peptide agonist dissociation and deactivation of adhesion G-protein-coupled receptors.bioRxiv : the preprint server for biology · 2024Article
- Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning.Molecules (Basel, Switzerland) · 2024Article
- Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists.bioRxiv : the preprint server for biology · 2024Article
- The Recognition Pathway of the SARS-CoV-2 Spike Receptor-Binding Domain to Human Angiotensin-Converting Enzyme 2.Molecules (Basel, Switzerland) · 2024Article
21 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions and biomolecular recognition.
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