Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models

Dejun Jiang, Chang‐Yu Hsieh, Guangyong Chen, +6

Journal of Cheminformatics

From machine learning to deep learning: Advances in scoring functions for protein–ligand docking

Chao Shen, Junjie Ding, Zhe Wang, +3

Wiley Interdisciplinary Reviews Computational Molecular Science

Drug TargetEngineeringMolecular BiologySystems PharmacologyProtein–ligand Docking +21

InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein–Ligand Interaction Predictions

Dejun Jiang, Chang‐Yu Hsieh, Yu Kang, +8

Journal of Medicinal Chemistry

Boosting Protein–Ligand Binding Pose Prediction and Virtual Screening Based on Residue–Atom Distance Likelihood Potential and Graph Transformer

Chao Shen, Xujun Zhang, Yafeng Deng, +6

Journal of Medicinal Chemistry

Protein-ligand Scoring FunctionsHit IdentificationBiomolecular Structure PredictionMolecular BiologyDocking-based Virtual Screening +16

Efficient and accurate large library ligand docking with KarmaDock

Xujun Zhang, Odin Zhang, Chao Shen, +16

Nature Computational Science

Large Library LigandMedicinal ChemistryMedicineNatural SciencesSmall Molecule Library +5

ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches

Tailong Lei, Chao Shen, Zhe Wang, +2

Journal of Chemical Information and Modeling

EngineeringMachine LearningHit IdentificationEnsemble Learning ModelsReliable Prediction +15

RELATION: A Deep Generative Model for Structure-Based De Novo Drug Design

Mingyang Wang, Chang‐Yu Hsieh, Jike Wang, +8

Journal of Medicinal Chemistry

Drug TargetRelation ModelEngineeringMolecular BiologyMolecular Design +15

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling

Odin Zhang, Jintu Zhang, Jieyu Jin, +11

Nature Machine Intelligence

EngineeringNatural SciencesComputational BiologyMolecular BiologyMolecular Generation Model +12

Beware of the generic machine learning-based scoring functions in structure-based virtual screening

Chao Shen, Ye Hu, Zhe Wang, +7

Briefings in Bioinformatics

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions

Chao Shen, Ye Hu, Zhe Wang, +7

Briefings in Bioinformatics