Deep learning in protein structural modeling and design

W Gao, SP Mahajan, J Sulam, JJ Gray - Patterns, 2020 - cell.com
Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and
powerful computational resources, impacting many fields, including protein structural …

MatGPT: A vane of materials informatics from past, present, to future

Z Wang, A Chen, K Tao, Y Han, J Li - Advanced Materials, 2024 - Wiley Online Library
Combining materials science, artificial intelligence (AI), physical chemistry, and other
disciplines, materials informatics is continuously accelerating the vigorous development of …

DeePMD-kit v2: A software package for deep potential models

J Zeng, D Zhang, D Lu, P Mo, Z Li, Y Chen… - The Journal of …, 2023 - pubs.aip.org
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics
simulations using machine learning potentials known as Deep Potential (DP) models. This …

Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensembles

AR Tan, S Urata, S Goldman, JCB Dietschreit… - npj Computational …, 2023 - nature.com
Neural networks (NNs) often assign high confidence to their predictions, even for points far
out of distribution, making uncertainty quantification (UQ) a challenge. When they are …

PW-SMD: A Plane-Wave Implicit Solvation Model Based on Electron Density for Surface Chemistry and Crystalline Systems in Aqueous Solution

Y Wang, C Teng, E Begin, M Bussiere… - Journal of Chemical …, 2024 - ACS Publications
Electron density-based implicit solvation models are a class of techniques for quantifying
solvation effects and calculating free energies of solvation without an explicit representation …

Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems

J Liu, X He - Wiley Interdisciplinary Reviews: Computational …, 2023 - Wiley Online Library
Quantum mechanical (QM) calculations are critical in quantitatively understanding the
relationship between the structure and physicochemical properties of various chemical …

Machine learning accelerates quantum mechanics predictions of molecular crystals

Y Han, I Ali, Z Wang, J Cai, S Wu, J Tang, L Zhang… - Physics Reports, 2021 - Elsevier
Quantum mechanics (QM) approaches (DFT, MP2, CCSD (T), etc.) play an important role in
calculating molecules and crystals with a high accuracy and acceptable efficiency. In recent …

Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications

T Morawietz, N Artrith - Journal of Computer-Aided Molecular Design, 2021 - Springer
Atomistic simulations have become an invaluable tool for industrial applications ranging
from the optimization of protein-ligand interactions for drug discovery to the design of new …

Ultra-fast and accurate binding energy prediction of shuttle effect-suppressive sulfur hosts for lithium-sulfur batteries using machine learning

H Zhang, Z Wang, J Ren, J Liu, J Li - Energy Storage Materials, 2021 - Elsevier
The shuttle effect of lithium polysulfides (LiPS) leads to fast capacity loss in lithium-sulfur
batteries, which hinders the practical applications and makes the discovery of shuttle effect …

Accelerated discovery of stable spinels in energy systems via machine learning

Z Wang, H Zhang, J Li - Nano Energy, 2021 - Elsevier
Discovery of new energy materials with thermal stability and special electro-optical
properties has always been the goal and challenge of material science. As an important …