The Potential of Neural Network Potentials

TT Duignan - ACS Physical Chemistry Au, 2024 - ACS Publications
In the next half-century, physical chemistry will likely undergo a profound transformation,
driven predominantly by the combination of recent advances in quantum chemistry and …

On the emergence of machine-learning methods in bottom-up coarse-graining

PG Sahrmann, GA Voth - Current Opinion in Structural Biology, 2025 - Elsevier
Machine-learning methods have gained significant attention in the computational chemistry
community as a viable approach to molecular modeling and analysis. Recent successes in …

Amaro: all heavy-atom transferable neural network potentials of protein thermodynamics

A Mirarchi, RP Peláez, G Simeon… - Journal of Chemical …, 2024 - ACS Publications
All-atom molecular simulations offer detailed insights into macromolecular phenomena, but
their substantial computational cost hinders the exploration of complex biological processes …

FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmap**

MS Jones, S Khanna, AL Ferguson - Journal of Chemical …, 2025 - ACS Publications
Coarse-grained models have become ubiquitous in biomolecular modeling tasks aimed at
studying slow dynamical processes such as protein folding and DNA hybridization. These …

Learning data efficient coarse-grained molecular dynamics from forces and noise

AEP Durumeric, Y Chen, F Noé, C Clementi - arxiv preprint arxiv …, 2024 - arxiv.org
Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for
modeling biomolecules. However, MLCG models currently require large amounts of data …

Modeling Boltzmann weighted structural ensembles of proteins using AI based methods

A Aranganathan, X Gu, D Wang, B Vani, P Tiwary - 2025 - chemrxiv.org
This review highlights recent advances in AI-driven methods for generating Boltzmann-
weighted structural ensembles, which are crucial for understanding biomolecular dynamics …

Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids

PG Sahrmann, GA Voth - Journal of Chemical Theory and …, 2024 - ACS Publications
A plethora of key biological events occur at the cellular membrane where the large
spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches …

Scalable emulation of protein equilibrium ensembles with generative deep learning

S Lewis, T Hempel, J Jiménez Luna, M Gastegger… - bioRxiv, 2024 - biorxiv.org
Following the sequence and structure revolutions, predicting the dynamical mechanisms of
proteins that implement biological function remains an outstanding scientific challenge …

Predicting solvation free energies with an implicit solvent machine learning potential

S Röcken, AF Burnet, J Zavadlav - arxiv preprint arxiv:2406.00183, 2024 - arxiv.org
Machine learning (ML) potentials are a powerful tool in molecular modeling, enabling ab
initio accuracy for comparably small computational costs. Nevertheless, all-atom simulations …

Transferable Boltzmann Generators

L Klein, F Noé - arxiv preprint arxiv:2406.14426, 2024 - arxiv.org
The generation of equilibrium samples of molecular systems has been a long-standing
problem in statistical physics. Boltzmann Generators are a generative machine learning …