Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries

C Selvaraj, I Chandra, SK Singh - Molecular diversity, 2021 - Springer
The global spread of COVID-19 has raised the importance of pharmaceutical drug
development as intractable and hot research. Developing new drug molecules to overcome …

Featurization strategies for protein–ligand interactions and their applications in scoring function development

G Xiong, C Shen, Z Yang, D Jiang, S Liu… - Wiley …, 2022 - Wiley Online Library
The predictive performance of classical scoring functions (SFs) seems to have reached a
plateau. Currently, SFs relying on sophisticated machine learning techniques have shown …

On the frustration to predict binding affinities from protein–ligand structures with deep neural networks

M Volkov, JA Turk, N Drizard, N Martin… - Journal of medicinal …, 2022 - ACS Publications
Accurate prediction of binding affinities from protein–ligand atomic coordinates remains a
major challenge in early stages of drug discovery. Using modular message passing graph …

[HTML][HTML] DTITR: End-to-end drug–target binding affinity prediction with transformers

NRC Monteiro, JL Oliveira, JP Arrais - Computers in Biology and Medicine, 2022 - Elsevier
The accurate identification of Drug–Target Interactions (DTIs) remains a critical turning point
in drug discovery and understanding of the binding process. Despite recent advances in …

Integrating Artificial Intelligence for Drug Discovery in the Context of Revolutionizing Drug Delivery

AI Visan, I Negut - Life, 2024 - mdpi.com
Drug development is expensive, time-consuming, and has a high failure rate. In recent
years, artificial intelligence (AI) has emerged as a transformative tool in drug discovery …

Artificial intelligence and cheminformatics tools: a contribution to the drug development and chemical science

I Saifi, BA Bhat, SS Hamdani, UY Bhat… - Journal of …, 2024 - Taylor & Francis
In the ever-evolving field of drug discovery, the integration of Artificial Intelligence (AI) and
Machine Learning (ML) with cheminformatics has proven to be a powerful combination …

Machine Learning for Sequence and Structure-Based Protein–Ligand Interaction Prediction

Y Zhang, S Li, K Meng, S Sun - Journal of Chemical Information …, 2024 - ACS Publications
Developing new drugs is too expensive and time-consuming. Accurately predicting the
interaction between drugs and targets will likely change how the drug is discovered …

Water network-augmented two-state model for protein–ligand binding affinity prediction

X Qu, L Dong, D Luo, Y Si, B Wang - Journal of Chemical …, 2023 - ACS Publications
Water network rearrangement from the ligand-unbound state to the ligand-bound state is
known to have significant effects on the protein–ligand binding interactions, but most of the …

Plas-5k: Dataset of protein-ligand affinities from molecular dynamics for machine learning applications

DB Korlepara, CS Vasavi, S Jeurkar, PK Pal, S Roy… - Scientific data, 2022 - nature.com
Computational methods and recently modern machine learning methods have played a key
role in structure-based drug design. Though several benchmarking datasets are available …

DOX_BDW: incorporating solvation and desolvation effects of cavity water into nonfitting protein–ligand binding affinity prediction

J Liu, J Wan, Y Ren, X Shao, X Xu… - Journal of Chemical …, 2023 - ACS Publications
Accurate prediction of the protein–ligand binding affinity (PLBA) with an affordable cost is
one of the ultimate goals in the field of structure-based drug design (SBDD), as well as a …