| Large-Scale Chemical Language Representations Capture Molecular Structure and Properties | Jun 17, 2021 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data | Jul 5, 2021 | AttributeDrug Discovery | CodeCode Available | 1 |
| Accelerating high-throughput virtual screening through molecular pool-based active learning | Dec 13, 2020 | Active LearningBayesian Optimization | CodeCode Available | 1 |
| DOCKSTRING: easy molecular docking yields better benchmarks for ligand design | Oct 29, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation | Apr 23, 2024 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer | Jan 22, 2021 | Drug DiscoveryMetric Learning | CodeCode Available | 1 |
| Activity Cliff Prediction: Dataset and Benchmark | Feb 15, 2023 | Drug DiscoveryPrediction | CodeCode Available | 1 |
| DrugAssist: A Large Language Model for Molecule Optimization | Dec 28, 2023 | Drug DiscoveryLanguage Modeling | CodeCode Available | 1 |
| Drug Discovery with Dynamic Goal-aware Fragments | Oct 2, 2023 | Drug Discovery | CodeCode Available | 1 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification | Jul 12, 2022 | Drug DiscoveryRelation Classification | CodeCode Available | 1 |
| Drug–target affinity prediction using graph neural network and contact maps | Jun 1, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction | Jun 6, 2021 | Drug DiscoveryProtein Interface Prediction | CodeCode Available | 1 |
| EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures | May 20, 2022 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| End-to-End Differentiable Molecular Mechanics Force Field Construction | Oct 2, 2020 | Computational chemistryDrug Discovery | CodeCode Available | 1 |
| Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language | Mar 6, 2023 | Activity PredictionAttribute | CodeCode Available | 1 |
| Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks | Nov 4, 2022 | Drug Discovery | CodeCode Available | 1 |
| Directional Message Passing for Molecular Graphs | Mar 6, 2020 | Drug DiscoveryFormation Energy | CodeCode Available | 1 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 |
| Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework | Dec 1, 2022 | Drug DiscoveryNER | CodeCode Available | 1 |
| Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design | Oct 12, 2021 | Drug Discovery | CodeCode Available | 1 |
| Automated 3D Pre-Training for Molecular Property Prediction | Jun 13, 2023 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Dec 4, 2024 | Contrastive LearningDrug Discovery | CodeCode Available | 1 |
| Extrapolative Controlled Sequence Generation via Iterative Refinement | Mar 8, 2023 | AttributeDrug Discovery | CodeCode Available | 1 |
| A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics | Jan 26, 2024 | Drug Discovery | CodeCode Available | 1 |
| Feature Overcorrelation in Deep Graph Neural Networks: A New Perspective | Jun 15, 2022 | Drug DiscoveryFeature Correlation | CodeCode Available | 1 |
| An adaptive graph learning method for automated molecular interactions and properties predictions | Jun 23, 2022 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| DeepNoise: Signal and Noise Disentanglement based on Classifying Fluorescent Microscopy Images via Deep Learning | Sep 13, 2022 | DisentanglementDrug Discovery | CodeCode Available | 1 |
| DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations | Jan 8, 2020 | Drug DiscoveryMolecular Docking | CodeCode Available | 1 |
| Forward Learning of Graph Neural Networks | Mar 16, 2024 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability | Oct 16, 2024 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation | Nov 4, 2023 | BenchmarkingDrug Discovery | CodeCode Available | 1 |
| Accurate ADMET Prediction with XGBoost | Apr 15, 2022 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| C5T5: Controllable Generation of Organic Molecules with Transformers | Aug 23, 2021 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| GeneDisco: A Benchmark for Experimental Design in Drug Discovery | Oct 22, 2021 | Active LearningDrug Discovery | CodeCode Available | 1 |
| Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning | Jun 2, 2023 | Drug Discovery | CodeCode Available | 1 |
| Discrete-state Continuous-time Diffusion for Graph Generation | May 19, 2024 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback | Nov 20, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity | Jan 18, 2022 | Drug Discovery | CodeCode Available | 1 |
| An effective self-supervised framework for learning expressive molecular global representations to drug discovery | May 3, 2021 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| DeepGG: a Deep Graph Generator | Jun 7, 2020 | Drug DiscoveryGraph Embedding | CodeCode Available | 1 |
| Cross-Domain Few-Shot Learning by Representation Fusion | Oct 13, 2020 | Cross-Domain Few-Shotcross-domain few-shot learning | CodeCode Available | 1 |
| DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction | Mar 31, 2020 | Drug DiscoveryRepresentation Learning | CodeCode Available | 1 |
| 3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery | Feb 7, 2025 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks | May 13, 2021 | BenchmarkingDrug Discovery | CodeCode Available | 1 |
| GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks | Mar 7, 2024 | Drug Discovery | CodeCode Available | 1 |
| GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation | Jan 26, 2020 | Density EstimationDrug Discovery | CodeCode Available | 1 |
| Graph Neural Networks for Quantifying Compatibility Mechanisms in Traditional Chinese Medicine | Nov 18, 2024 | Drug DiscoveryFeature Engineering | CodeCode Available | 1 |
| Context-enriched molecule representations improve few-shot drug discovery | Apr 24, 2023 | Drug DiscoveryFew-Shot Learning | CodeCode Available | 1 |
| Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation | Jan 1, 2023 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
