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 …
driven predominantly by the combination of recent advances in quantum chemistry and …
On the emergence of machine-learning methods in bottom-up coarse-graining
Machine-learning methods have gained significant attention in the computational chemistry
community as a viable approach to molecular modeling and analysis. Recent successes in …
community as a viable approach to molecular modeling and analysis. Recent successes in …
Amaro: all heavy-atom transferable neural network potentials of protein thermodynamics
All-atom molecular simulations offer detailed insights into macromolecular phenomena, but
their substantial computational cost hinders the exploration of complex biological processes …
their substantial computational cost hinders the exploration of complex biological processes …
FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmap**
Coarse-grained models have become ubiquitous in biomolecular modeling tasks aimed at
studying slow dynamical processes such as protein folding and DNA hybridization. These …
studying slow dynamical processes such as protein folding and DNA hybridization. These …
Learning data efficient coarse-grained molecular dynamics from forces and noise
Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for
modeling biomolecules. However, MLCG models currently require large amounts of data …
modeling biomolecules. However, MLCG models currently require large amounts of data …
Modeling Boltzmann weighted structural ensembles of proteins using AI based methods
This review highlights recent advances in AI-driven methods for generating Boltzmann-
weighted structural ensembles, which are crucial for understanding biomolecular dynamics …
weighted structural ensembles, which are crucial for understanding biomolecular dynamics …
Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids
A plethora of key biological events occur at the cellular membrane where the large
spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches …
spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches …
Scalable emulation of protein equilibrium ensembles with generative deep learning
Following the sequence and structure revolutions, predicting the dynamical mechanisms of
proteins that implement biological function remains an outstanding scientific challenge …
proteins that implement biological function remains an outstanding scientific challenge …
Predicting solvation free energies with an implicit solvent machine learning potential
Machine learning (ML) potentials are a powerful tool in molecular modeling, enabling ab
initio accuracy for comparably small computational costs. Nevertheless, all-atom simulations …
initio accuracy for comparably small computational costs. Nevertheless, all-atom simulations …
Transferable Boltzmann Generators
The generation of equilibrium samples of molecular systems has been a long-standing
problem in statistical physics. Boltzmann Generators are a generative machine learning …
problem in statistical physics. Boltzmann Generators are a generative machine learning …