AI Methods for Antimicrobial Peptides: Progress and Challenges

CA Brizuela, G Liu, JM Stokes… - Microbial …, 2025 - Wiley Online Library
Antimicrobial peptides (AMPs) are promising candidates to combat multidrug‐resistant
pathogens. However, the high cost of extensive wet‐lab screening has made AI methods for …

AI-driven inverse design of materials: Past, present and future

XQ Han, XD Wang, MY Xu, Z Feng, BW Yao… - Chinese Physics …, 2024 - iopscience.iop.org
The discovery of advanced materials is the cornerstone of human technological
development and progress. The structures of materials and their corresponding properties …

Improving equivariant graph neural networks on large geometric graphs via virtual nodes learning

Y Zhang, J Cen, J Han, Z Zhang, J Zhou… - Forty-first International …, 2024 - openreview.net
Equivariant Graph Neural Networks (GNNs) have made remarkable success in a variety of
scientific applications. However, existing equivariant GNNs encounter the efficiency issue for …

Crystalline material discovery in the era of artificial intelligence

Z Wang, H Hua, W Lin, M Yang, KC Tan - arxiv preprint arxiv:2408.08044, 2024 - arxiv.org
Crystalline materials, with their symmetrical and periodic structures, possess a diverse array
of properties and have been widely used in various fields, ranging from electronic devices to …

Scalable crystal structure relaxation using an iteration-free deep generative model with uncertainty quantification

Z Yang, YM Zhao, X Wang, X Liu, X Zhang, Y Li… - Nature …, 2024 - nature.com
In computational molecular and materials science, determining equilibrium structures is the
crucial first step for accurate subsequent property calculations. However, the recent …

Efficient equivariant model for machine learning interatomic potentials

Z Yang, X Wang, Y Li, Q Lv, CYC Chen… - npj Computational …, 2025 - nature.com
In modern computational materials, machine learning has shown the capability to predict
interatomic potentials, thereby supporting and accelerating conventional molecular …

Graph Neural Network-Based Molecular Property Prediction with Patch Aggregation

TJ See, D Zhang, M Boley… - Journal of Chemical …, 2024 - ACS Publications
Graph neural networks (GNNs) have emerged as powerful tools for quantum chemical
property prediction, leveraging the inherent graph structure of molecular systems. GNNs …

Scaling Graph Neural Networks to Large Proteins

J Airas, B Zhang - Journal of Chemical Theory and Computation, 2024 - ACS Publications
Graph neural network (GNN) architectures have emerged as promising force field models,
exhibiting high accuracy in predicting complex energies and forces based on atomic …

Learning local equivariant representations for quantum operators

Z Zhouyin, Z Gan, MK Liu, SK Pandey, L Zhang… - arxiv preprint arxiv …, 2024 - arxiv.org
Predicting quantum operator matrices such as Hamiltonian, overlap, and density matrices in
the density functional theory (DFT) framework is crucial for material science. Current …

Improved and Interpretable Prediction of Cytochrome P450-Mediated Metabolism by Molecule-Level Graph Modeling and Subgraph Information Bottlenecks

Y Li, QW Xu, GL Jian, XL Zhang… - Journal of Chemical …, 2024 - ACS Publications
Accurately identifying sites of metabolism (SoM) mediated by cytochrome P450 (CYP)
enzymes, which are responsible for drug metabolism in the body, is critical in the early stage …