AIMC Topic: Drug Discovery

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A meta-learning framework to mitigate negative transfer in transfer learning applicable to drug design.

Scientific reports
Data sparseness is a major limiting factor for deep machine learning. In the natural sciences, data distributions are heterogeneous. For instance, in chemistry and early-phase drug discovery, compound and molecular property data are typically sparse ...

Predicting drug-target affinity through triple pre-activated random residual planet convolution coupled attention network and contact maps.

Journal of computer-aided molecular design
Drug discovery relies on the ability to predict drug-target affinity (DTA), which allows for the efficient identification of drug candidates for certain protein targets. Scalability, accuracy, and interpretability are issues that traditional methods ...

Enabling Open Machine Learning of Deoxyribonucleic Acid-Encoded Library Selections to Accelerate the Discovery of Small Molecule Protein Binders.

Journal of medicinal chemistry
Machine learning (ML) is increasingly used in DNA-encoded library (DEL) screening for ligand discovery, but its success depends on access to suitable data sets, which are often proprietary and costly. To overcome this, we present the first fully open...

Developing a predictive QSAR model for FGFR-1 inhibitors: integrating computational and experimental validation.

Journal of computer-aided molecular design
The traditional drug discovery process is often lengthy, costly, and characterized by a high failure rate. There is a pressing need for innovative strategies to optimize this process and improve the chances of identifying effective therapeutic candid...

ML-PLA: Enhancing Protein-Ligand Binding Affinity Prediction with Microenvironment and Long-Range Interaction-Aware Graph Neural Networks.

Journal of chemical information and modeling
Accurately predicting protein-ligand binding affinity (PLA) is essential in drug discovery for identifying lead compounds. The sequence and structural contexts of an amino acid residue (i.e., microenvironment) describe the surrounding chemical proper...

Graph based link prediction for epilepsy drug discovery.

Scientific reports
Epilepsy is one of the most prevalent neurological disorders, affecting approximately 23 million people in Asia alone. It is a disorder with severe social impacts and is going to progressively damage the brain. It encompasses a wide range of syndrome...

A comprehensive application of FiveFold for conformation ensemble-based protein structure prediction.

Scientific reports
The emergence of artificial intelligence in protein structure prediction has significantly advanced our understanding of protein folding. Yet, challenges remain in accurately modeling intrinsically disordered proteins (IDPs) and capturing conformatio...

Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles.

Journal of computer-aided molecular design
Kinase profiling is an essential step in both hit identification and selectivity evaluation. Since in vitro testing of large chemical libraries is costly and time-consuming, a computational approach can be applied to narrow down the reasonable chemic...

MaskMol: knowledge-guided molecular image pre-training framework for activity cliffs with pixel masking.

BMC biology
BACKGROUND: Activity cliffs, which refer to pairs of molecules that are structurally similar but show significant differences in their potency, can lead to model representation collapse and make the model challenging to distinguish them.

Auxiliary Discrminator Sequence Generative Adversarial Networks for Few Sample Molecule Generation.

Journal of chemical information and modeling
In this work, we introduce auxiliary discriminator sequence generative adversarial networks (ADSeqGAN), a novel approach for molecular generation in small-sample data sets. Traditional generative models often struggle with limited training data, part...