Neighborhood complex based machine learning (NCML) models for drug design

X Liu, K Xia - Interpretability of Machine Intelligence in Medical …, 2021 - Springer
The importance of drug design cannot be overemphasized. Recently, artificial intelligence
(AI) based drug design has begun to gain momentum due to the great advancement in …

An ensemble‐based approach to estimate confidence of predicted protein–ligand binding affinity values

M Rayka, M Mirzaei… - Molecular Informatics, 2024 - Wiley Online Library
When designing a machine learning‐based scoring function, we access a limited number of
protein‐ligand complexes with experimentally determined binding affinity values …

Specifics of metabolite-protein interactions and their computational analysis and prediction

D Walther - Cell-Wide Identification of Metabolite-Protein …, 2022 - Springer
Computational approaches to the characterization and prediction of compound-protein
interactions have a long research history and are well established, driven primarily by the …

[HTML][HTML] AI-based prediction of protein–ligand binding affinity and discovery of potential natural product inhibitors against ERK2

R Yang, L Zhang, F Bu, F Sun, B Cheng - BMC chemistry, 2024 - Springer
Determination of protein–ligand binding affinity (PLA) is a key technological tool in hit
discovery and lead optimization, which is critical to the drug development process. PLA can …

[HTML][HTML] Modeling DTA by Combining Multiple-Instance Learning with a Private-Public Mechanism

C Wang, Y Chen, L Zhao, J Wang, N Wen - International Journal of …, 2022 - mdpi.com
The prediction of the strengths of drug–target interactions, also called drug–target binding
affinities (DTA), plays a fundamental role in facilitating drug discovery, where the goal is to …

Drug-Target Binding Affinity Prediction in a Continuous Latent Space Using Variational Autoencoders

L Zhao, Y Zhu, N Wen, C Wang… - … /ACM Transactions on …, 2024 - ieeexplore.ieee.org
Accurate prediction of Drug-Target binding Affinity (DTA) is a daunting yet pivotal task in the
sphere of drug discovery. Over the years, a plethora of deep learning-based DTA models …

DPLA: prediction of protein-ligand binding affinity by integrating multi-level information

W Wang, B Sun, D Liu, X Wang… - 2021 IEEE International …, 2021 - ieeexplore.ieee.org
In the drug discovery process and repurposing of existing drugs, accurately identifying
ligands with high binding affinity to proteins is a very critical step. However, it sinks a lot of …

HSGCL-DTA: Hybrid-scale Graph Contrastive Learning based Drug-Target Binding Affinity Prediction

H Ye, Y Song, B Wang, L Wu, S He… - 2023 IEEE 35th …, 2023 - ieeexplore.ieee.org
Drug-target binding affinity (DTA) is a critical criterion for drug screening. Accurate affinity
prediction will significantly cut the cost of new drug development and accelerate the drug …

PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction.

Y Zhang, C Zhou - Journal of Bioinformatics and Computational …, 2024 - europepmc.org
Biomolecular interaction recognition between ligands and proteins is an essential task,
which largely enhances the safety and efficacy in drug discovery and development stage …

Predicting Protein-Ligand Binding Affinity with Multi-Scale Structural Features

H Wang, J Zhao, S Wang, Z He… - … on Bioinformatics and …, 2023 - ieeexplore.ieee.org
Predicting protein-ligand binding affinity is important in areas such as drug discovery, gene
regulation and signal transduction. The DTA (Drug-Target Affinity) method based on protein …