Accelerators for classical molecular dynamics simulations of biomolecules

D Jones, JE Allen, Y Yang… - Journal of chemical …, 2022 - ACS Publications
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model
biomolecular structures such as proteins and their interactions with drug-like small …

Deep molecular representation learning via fusing physical and chemical information

S Yang, Z Li, G Song, L Cai - Advances in Neural …, 2021 - proceedings.neurips.cc
Molecular representation learning is the first yet vital step in combining deep learning and
molecular science. To push the boundaries of molecular representation learning, we present …

Discovery of Dual Ion-Electron Conductivity of Metal–Organic Frameworks via Machine Learning-Guided Experimentation

R Bashiri, PS Lawson, S He, S Nanayakkara… - Chemistry of …, 2025 - ACS Publications
Identifying conductive metal–organic frameworks (MOFs) with a coupled ion-electron
behavior from a vast array of existing MOFs offers a cost-effective strategy to tap into their …

HDBind: encoding of molecular structure with hyperdimensional binary representations

D Jones, X Zhang, BJ Bennion, S **e, W Xu… - Scientific Reports, 2024 - nature.com
Traditional methods for identifying “hit” molecules from a large collection of potential drug-
like candidates rely on biophysical theory to compute approximations to the Gibbs free …

Small molecules targeting SARS-CoV-2 spike glycoprotein receptor-binding domain

Y Rodriguez, SM Cardoze, OW Obineche, C Melo… - ACS …, 2022 - ACS Publications
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the
coronavirus disease 2019 (COVID-19) pandemic. Several variants of SARS-CoV-2 have …

Clustering protein binding pockets and identifying potential drug interactions: a novel ligand-based featurization method

GA Stevenson, D Kirshner, BJ Bennion… - Journal of Chemical …, 2023 - ACS Publications
Protein–ligand interactions are essential to drug discovery and drug development efforts.
Desirable on-target or multitarget interactions are the first step in finding an effective …

Scalable composition and analysis techniques for massive scientific workflows

DH Ahn, X Zhang, J Mast, S Herbein… - 2022 IEEE 18th …, 2022 - ieeexplore.ieee.org
Composite science workflows are gaining traction to manage the combined effects of (1)
extreme hardware heterogeneity in new High Performance Computing (HPC) systems and …

Step** Back to SMILES transformers for fast molecular representation inference

W Zhu, Z Li, L Cai, G Song - arxiv preprint arxiv:2112.13305, 2021 - arxiv.org
In the intersection of molecular science and deep learning, tasks like virtual screening have
driven the need for a high-throughput molecular representation generator on large chemical …

[HTML][HTML] Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction

YJ Fan, JE Allen, KS McLoughlin, D Shi… - Artificial intelligence …, 2023 - Elsevier
Neural Network (NN) models provide potential to speed up the drug discovery process and
reduce its failure rates. The success of NN models requires uncertainty quantification (UQ) …

Masked molecule modeling: a new paradigm of molecular representation learning for chemistry understanding

J He, K Tian, S Luo, Y Min, S Zheng, Y Shi, D He, H Liu… - 2022 - researchsquare.com
Molecular representation learning is essential to deep learning for chemistry, where the
molecules are embedded into continuous real-valued vectors as better representations in …