AIMC Topic: Drug Discovery

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GR-pKa: a message-passing neural network with retention mechanism for pKa prediction.

Briefings in bioinformatics
During the drug discovery and design process, the acid-base dissociation constant (pKa) of a molecule is critically emphasized due to its crucial role in influencing the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties...

MetaPredictor: in silico prediction of drug metabolites based on deep language models with prompt engineering.

Briefings in bioinformatics
Metabolic processes can transform a drug into metabolites with different properties that may affect its efficacy and safety. Therefore, investigation of the metabolic fate of a drug candidate is of great significance for drug discovery. Computational...

ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries.

Bioinformatics (Oxford, England)
MOTIVATION: The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded the chemical diversity of small molecules for drug discovery. Selecting compound...

OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs.

Bioinformatics (Oxford, England)
MOTIVATION: Deep graph learning (DGL) has been widely employed in the realm of ligand-based virtual screening. Within this field, a key hurdle is the existence of activity cliffs (ACs), where minor chemical alterations can lead to significant changes...

GEMF: a novel geometry-enhanced mid-fusion network for PLA prediction.

Briefings in bioinformatics
Accurate prediction of protein-ligand binding affinity (PLA) is important for drug discovery. Recent advances in applying graph neural networks have shown great potential for PLA prediction. However, existing methods usually neglect the geometric inf...

Morphological profiling for drug discovery in the era of deep learning.

Briefings in bioinformatics
Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the sin...

Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides.

Briefings in bioinformatics
With their diverse biological activities, peptides are promising candidates for therapeutic applications, showing antimicrobial, antitumour and hormonal signalling capabilities. Despite their advantages, therapeutic peptides face challenges such as s...

Prediction of drug-protein interaction based on dual channel neural networks with attention mechanism.

Briefings in functional genomics
The precise identification of drug-protein inter action (DPI) can significantly speed up the drug discovery process. Bioassay methods are time-consuming and expensive to screen for each pair of drug proteins. Machine-learning-based methods cannot acc...

Molecular property prediction based on graph structure learning.

Bioinformatics (Oxford, England)
MOTIVATION: Molecular property prediction (MPP) is a fundamental but challenging task in the computer-aided drug discovery process. More and more recent works employ different graph-based models for MPP, which have achieved considerable progress in i...