ReviewThe European physical journal. B2021
Collective variable-based enhanced sampling and machine learning.
Review in The European physical journal. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- First principles reactive flux theory for surface reactions revealing multiple channels and recrossing dynamics.Nature communications · 2026Article
- Reactive Machine Learning Interatomic Potentials for Chemistry and Materials Science.Chemical reviews · 2026Review
- Assessing the Performance of BioEmu in Understanding Protein Dynamics.International journal of molecular sciences · 2026Article
- Selector: A General Python Library for Diverse Subset Selection.Journal of chemical information and modeling · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Advanced Computational Methods in Protein Simulations: A Case Study of Enhanced Sampling Applied to Membrane Transporters.Advances in experimental medicine and biology · 2026Review
- Selector: A General Python Library for Diverse Subset Selection.bioRxiv : the preprint server for biology · 2025Article
- NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks.Journal of chemical information and modeling · 2025Article
- Accelerating Molecular Dynamics through Informed Resetting.Journal of chemical theory and computation · 2025Article
- Unsupervised learning of collective variables for conformational sampling of cyclic peptides.Methods in enzymology · 2025Article
- Correlating enzymatic reactivity for different substrates using transferable data-driven collective variables.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Adaptive CVgen: Leveraging reinforcement learning for advanced sampling in protein folding and chemical reactions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.Journal of chemical theory and computation · 2024Article
- Automated collective variable discovery for MFSD2A transporter from molecular dynamics simulations.Biophysical journal · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Short-Time Infrequent Metadynamics for Improved Kinetics Inference.Journal of chemical theory and computation · 2024Article
- One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates.The journal of physical chemistry. B · 2024Article
- Effective data-driven collective variables for free energy calculations from metadynamics of paths.PNAS nexus · 2024Article
- tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation.Journal of chemical theory and computation · 2023Article
- Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.Journal of chemical information and modeling · 2023Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
abstractCollective variable-based enhanced sampling methods have been widely used to study thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced sampling methods are affected by two factors: constructing appropriate collective variables for enhanced sampling and generating accurate free energy surfaces. Recently, many machine learning techniques have been developed to improve the quality of collective variables and the accuracy of free energy surfaces. Although machine learning has achieved great successes in improving enhanced sampling methods, there are still many challenges and open questions. In this perspective, we shall review recent developments on integrating machine learning techniques and collective variable-based enhanced sampling approaches. We also discuss challenges and future research directions including generating kinetic information, exploring high-dimensional free energy surfaces, and efficiently sampling all-atom configurations. GRAPHIC ABSTRACT:
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Registered trials
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.