Geometric deep learning for drug discovery

M Liu, C Li, R Chen, D Cao, X Zeng - Expert Systems with Applications, 2024 - Elsevier
Drug discovery is a time-consuming and expensive process. With the development of
Artificial Intelligence (AI) techniques, molecular Geometric Deep Learning (GDL) has …

[HTML][HTML] Protein representations: Encoding biological information for machine learning in biocatalysis

D Harding-Larsen, J Funk, NG Madsen… - Biotechnology …, 2024 - Elsevier
Enzymes offer a more environmentally friendly and low-impact solution to conventional
chemistry, but they often require additional engineering for their application in industrial …

DeepCompoundNet: enhancing compound–protein interaction prediction with multimodal convolutional neural networks

F Palhamkhani, M Alipour, A Dehnad… - Journal of …, 2025 - Taylor & Francis
Virtual screening has emerged as a valuable computational tool for predicting compound–
protein interactions, offering a cost-effective and rapid approach to identifying potential …

Efficient deep model ensemble framework for drug-target interaction prediction

J Wei, Y Zhu, L Zhuo, Y Liu, X Fu… - The Journal of Physical …, 2024 - ACS Publications
Accurate prediction of Drug-Target Interactions (DTI) is crucial for drug development. Current
state-of-the-art deep learning methods have significantly advanced the field; however, these …

Binding affinity predictions with hybrid quantum-classical convolutional neural networks

L Domingo, M Djukic, C Johnson, F Borondo - Scientific Reports, 2023 - nature.com
Central in drug design is the identification of biomolecules that uniquely and robustly bind to
a target protein, while minimizing their interactions with others. Accordingly, precise binding …

A systematic survey in geometric deep learning for structure-based drug design

Z Zhang, J Yan, Q Liu, E Chen, M Zitnik - arxiv preprint arxiv:2306.11768, 2023 - arxiv.org
Structure-based drug design (SBDD) utilizes the three-dimensional geometry of proteins to
identify potential drug candidates. Traditional methods, grounded in physicochemical …

Data‐Driven Protein Engineering for Improving Catalytic Activity and Selectivity

YF Ao, M Dörr, MJ Menke, S Born, E Heuson… - …, 2024 - Wiley Online Library
Protein engineering is essential for altering the substrate scope, catalytic activity and
selectivity of enzymes for applications in biocatalysis. However, traditional approaches, such …

Ammvf-dti: A novel model predicting drug–target interactions based on attention mechanism and multi-view fusion

L Wang, Y Zhou, Q Chen - International Journal of Molecular Sciences, 2023 - mdpi.com
Accurate identification of potential drug–target interactions (DTIs) is a crucial task in drug
development and repositioning. Despite the remarkable progress achieved in recent years …

Leak proof PDBBind: A reorganized dataset of protein-ligand complexes for more generalizable binding affinity prediction

J Li, X Guan, O Zhang, K Sun, Y Wang, D Bagni… - Ar**v, 2024 - pmc.ncbi.nlm.nih.gov
Many physics-based and machine-learned scoring functions (SFs) used to predict protein-
ligand binding free energies have been trained on the PDBBind dataset. However, it is …

SS-GNN: a simple-structured graph neural network for affinity prediction

S Zhang, Y **, T Liu, Q Wang, Z Zhang, S Zhao… - ACS …, 2023 - ACS Publications
Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due
to the limited computational resources in practical applications and is a crucial basis for drug …