Comprehensive survey of recent drug discovery using deep learning

J Kim, S Park, D Min, W Kim - International Journal of Molecular Sciences, 2021 - mdpi.com
Drug discovery based on artificial intelligence has been in the spotlight recently as it
significantly reduces the time and cost required for developing novel drugs. With the …

[HTML][HTML] Advancing drug discovery with deep attention neural networks

A Lavecchia - Drug Discovery Today, 2024 - Elsevier
In the dynamic field of drug discovery, deep attention neural networks are revolutionizing our
approach to complex data. This review explores the attention mechanism and its extended …

XGraphBoost: extracting graph neural network-based features for a better prediction of molecular properties

D Deng, X Chen, R Zhang, Z Lei… - Journal of chemical …, 2021 - ACS Publications
Determining the properties of chemical molecules is essential for screening candidates
similar to a specific drug. These candidate molecules are further evaluated for their target …

Fractional denoising for 3d molecular pre-training

S Feng, Y Ni, Y Lan, ZM Ma… - … Conference on Machine …, 2023 - proceedings.mlr.press
Coordinate denoising is a promising 3D molecular pre-training method, which has achieved
remarkable performance in various downstream drug discovery tasks. Theoretically, the …

Multilingual molecular representation learning via contrastive pre-training

Z Guo, P Sharma, A Martinez, L Du… - arXiv preprint arXiv …, 2021 - arxiv.org
Molecular representation learning plays an essential role in cheminformatics. Recently,
language model-based approaches have gained popularity as an alternative to traditional …

Automating genetic algorithm mutations for molecules using a masked language model

AE Blanchard, MC Shekar, S Gao… - IEEE Transactions …, 2022 - ieeexplore.ieee.org
Inspired by the evolution of biological systems, genetic algorithms have been applied to
generate solutions for optimization problems in a variety of scientific and engineering …

Unimap: universal smiles-graph representation learning

S Feng, L Yang, W Ma, Y Lan - arXiv preprint arXiv:2310.14216, 2023 - arxiv.org
Molecular representation learning is fundamental for many drug related applications. Most
existing molecular pre-training models are limited in using single molecular modality, either …

Multi-Scale Protein Language Model for Unified Molecular Modeling

K Zheng, S Long, T Lu, J Yang, X Dai, M Zhang, Z Nie… - bioRxiv, 2024 - biorxiv.org
Protein language models have demonstrated significant potential in the field of protein
engineering. However, current protein language models primarily operate at the residue …

Advancing Drug-Target Interactions Prediction: Leveraging a Large-Scale Dataset with a Rapid and Robust Chemogenomic Algorithm

G Guichaoua, P Pinel, B Hoffmann, CA Azencott… - bioRxiv, 2024 - biorxiv.org
Predicting drug-target interactions (DTIs) is crucial for drug discovery, and heavily relies on
supervised learning techniques. Supervised learning algorithms for DTI prediction use …

ESM All-Atom: Multi-Scale Protein Language Model for Unified Molecular Modeling

K Zheng, S Long, T Lu, J Yang, X Dai, M Zhang… - Forty-first International … - openreview.net
Protein language models have demonstrated significant potential in the field of protein
engineering. However, current protein language models primarily operate at the residue …