Integrated molecular modeling and machine learning for drug design

S Xia, E Chen, Y Zhang - Journal of chemical theory and …, 2023 - ACS Publications
Modern therapeutic development often involves several stages that are interconnected, and
multiple iterations are usually required to bring a new drug to the market. Computational …

Boosting protein–ligand binding pose prediction and virtual screening based on residue–atom distance likelihood potential and graph transformer

C Shen, X Zhang, Y Deng, J Gao, D Wang… - Journal of Medicinal …, 2022 - ACS Publications
The past few years have witnessed enormous progress toward applying machine learning
approaches to the development of protein–ligand scoring functions. However, the robust …

Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design

HYI Lam, R Pincket, H Han, XE Ong, Z Wang… - Nature Machine …, 2023 - nature.com
Although there has been considerable progress in molecular property prediction in
computer-aided drug design, there is a critical need to have fast and accurate models. Many …

Geometric interaction graph neural network for predicting protein–ligand binding affinities from 3d structures (gign)

Z Yang, W Zhong, Q Lv, T Dong… - The journal of physical …, 2023 - ACS Publications
Predicting protein–ligand binding affinities (PLAs) is a core problem in drug discovery.
Recent advances have shown great potential in applying machine learning (ML) for PLA …

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

K Jiang, H Guo, J Zhai - Journal of Integrative Plant Biology, 2023 - Wiley Online Library
Both phytohormone signaling and epigenetic mechanisms have long been known to play
crucial roles in plant development and plasticity in response to ambient stimuli. Indeed …

A generalized protein–ligand scoring framework with balanced scoring, docking, ranking and screening powers

C Shen, X Zhang, CY Hsieh, Y Deng, D Wang, L Xu… - Chemical …, 2023 - pubs.rsc.org
Applying machine learning algorithms to protein–ligand scoring functions has aroused
widespread attention in recent years due to the high predictive accuracy and affordable …

Multiscale topology-enabled structure-to-sequence transformer for protein–ligand interaction predictions

D Chen, J Liu, GW Wei - Nature Machine Intelligence, 2024 - nature.com
Despite the success of pretrained natural language processing (NLP) models in various
fields, their application in computational biology has been hindered by their reliance on …

Hac-net: A hybrid attention-based convolutional neural network for highly accurate protein–ligand binding affinity prediction

GW Kyro, RI Brent, VS Batista - Journal of Chemical Information …, 2023 - ACS Publications
Applying deep learning concepts from image detection and graph theory has greatly
advanced protein–ligand binding affinity prediction, a challenge with enormous ramifications …

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function

Z Wang, L Zheng, S Wang, M Lin, Z Wang… - Briefings in …, 2023 - academic.oup.com
The recently reported machine learning-or deep learning-based scoring functions (SFs)
have shown exciting performance in predicting protein–ligand binding affinities with fruitful …

Conserved sites and recognition mechanisms of T1R1 and T2R14 receptors revealed by ensemble docking and molecular descriptors and fingerprints combined with …

Z Cui, N Zhang, T Zhou, X Zhou, H Meng… - Journal of Agricultural …, 2023 - ACS Publications
Taste peptides, as an important component of protein-rich foodstuffs, potentiate the nutrition
and taste of food. Thereinto, umami-and bitter-taste peptides have been ex tensively …