Deep learning methods for molecular representation and property prediction

Z Li, M Jiang, S Wang, S Zhang - Drug Discovery Today, 2022 - Elsevier
Highlights•The deep learning method could effectively represent the molecular structure and
predict molecular property through diversified models.•One, two, and three-dimensional …

A practical guide to machine-learning scoring for structure-based virtual screening

VK Tran-Nguyen, M Junaid, S Simeon, PJ Ballester - Nature Protocols, 2023 - nature.com
Abstract Structure-based virtual screening (SBVS) via docking has been used to discover
active molecules for a range of therapeutic targets. Chemical and protein data sets that …

GNINA 1.0: molecular docking with deep learning

AT McNutt, P Francoeur, R Aggarwal, T Masuda… - Journal of …, 2021 - Springer
Molecular docking computationally predicts the conformation of a small molecule when
binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline …

Artificial intelligence in the battle against coronavirus (COVID-19): a survey and future research directions

TT Nguyen, QVH Nguyen, DT Nguyen, S Yang… - arxiv preprint arxiv …, 2020 - arxiv.org
Artificial intelligence (AI) has been applied widely in our daily lives in a variety of ways with
numerous success stories. AI has also contributed to dealing with the coronavirus disease …

Algebraic graph-assisted bidirectional transformers for molecular property prediction

D Chen, K Gao, DD Nguyen, X Chen, Y Jiang… - Nature …, 2021 - nature.com
The ability of molecular property prediction is of great significance to drug discovery, human
health, and environmental protection. Despite considerable efforts, quantitative prediction of …

Deep learning in virtual screening: recent applications and developments

TB Kimber, Y Chen, A Volkamer - International journal of molecular …, 2021 - mdpi.com
Drug discovery is a cost and time-intensive process that is often assisted by computational
methods, such as virtual screening, to speed up and guide the design of new compounds …

COVID-19 and SARS-CoV-2. Modeling the present, looking at the future

E Estrada - Physics reports, 2020 - Elsevier
Abstract Since December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2
(SARS-CoV-2) has produced an outbreak of pulmonary disease which has soon become a …

Position: Topological deep learning is the new frontier for relational learning

T Papamarkou, T Birdal, M Bronstein… - arxiv preprint arxiv …, 2024 - arxiv.org
Topological deep learning (TDL) is a rapidly evolving field that uses topological features to
understand and design deep learning models. This paper posits that TDL is the new frontier …

Persistent spectral–based machine learning (PerSpect ML) for protein-ligand binding affinity prediction

Z Meng, K **a - Science advances, 2021 - science.org
Molecular descriptors are essential to not only quantitative structure-activity relationship
(QSAR) models but also machine learning–based material, chemical, and biological data …

Topological feature engineering for machine learning based halide perovskite materials design

DV Anand, Q Xu, JJ Wee, K **a, TC Sum - npj Computational Materials, 2022 - nature.com
Accelerated materials development with machine learning (ML) assisted screening and high
throughput experimentation for new photovoltaic materials holds the key to addressing our …