Structure-based drug design with geometric deep learning

C Isert, K Atz, G Schneider - Current Opinion in Structural Biology, 2023 - Elsevier
Abstract Structure-based drug design uses three-dimensional geometric information of
macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric …

The central role of density functional theory in the AI age

B Huang, GF von Rudorff, OA von Lilienfeld - Science, 2023 - science.org
Density functional theory (DFT) plays a pivotal role in chemical and materials science
because of its relatively high predictive power, applicability, versatility, and computational …

Accurate global machine learning force fields for molecules with hundreds of atoms

S Chmiela, V Vassilev-Galindo, OT Unke… - Science …, 2023 - science.org
Global machine learning force fields, with the capacity to capture collective interactions in
molecular systems, now scale up to a few dozen atoms due to considerable growth of model …

A Euclidean transformer for fast and stable machine learned force fields

JT Frank, OT Unke, KR Müller, S Chmiela - Nature Communications, 2024 - nature.com
Recent years have seen vast progress in the development of machine learned force fields
(MLFFs) based on ab-initio reference calculations. Despite achieving low test errors, the …

MACE-OFF23: Transferable machine learning force fields for organic molecules

DP Kovács, JH Moore, NJ Browning, I Batatia… - arxiv preprint arxiv …, 2023 - arxiv.org
Classical empirical force fields have dominated biomolecular simulation for over 50 years.
Although widely used in drug discovery, crystal structure prediction, and biomolecular …

Machine learned coarse-grained protein force-fields: Are we there yet?

AEP Durumeric, NE Charron, C Templeton… - Current opinion in …, 2023 - Elsevier
The successful recent application of machine learning methods to scientific problems
includes the learning of flexible and accurate atomic-level force-fields for materials and …

Scaling the leading accuracy of deep equivariant models to biomolecular simulations of realistic size

B Kozinsky, A Musaelian, A Johansson… - Proceedings of the …, 2023 - dl.acm.org
This work brings the leading accuracy, sample efficiency, and robustness of deep
equivariant neural networks to the extreme computational scale. This is achieved through a …

Machine learning coarse-grained potentials of protein thermodynamics

M Majewski, A Pérez, P Thölke, S Doerr… - Nature …, 2023 - nature.com
A generalized understanding of protein dynamics is an unsolved scientific problem, the
solution of which is critical to the interpretation of the structure-function relationships that …

Ab initio characterization of protein molecular dynamics with AI2BMD

T Wang, X He, M Li, Y Li, R Bi, Y Wang, C Cheng… - Nature, 2024 - nature.com
Biomolecular dynamics simulation is a fundamental technology for life sciences research,
and its usefulness depends on its accuracy and efficiency,–. Classical molecular dynamics …

Prospective de novo drug design with deep interactome learning

K Atz, L Cotos, C Isert, M Håkansson, D Focht… - Nature …, 2024 - nature.com
De novo drug design aims to generate molecules from scratch that possess specific
chemical and pharmacological properties. We present a computational approach utilizing …