| Geometric Deep Learning for Structure-Based Drug Design: A Survey | Jun 20, 2023 | BenchmarkingDeep Learning | CodeCode Available | 1 |
| DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data | Jul 5, 2021 | AttributeDrug Discovery | CodeCode Available | 1 |
| Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer | Jan 22, 2021 | Drug DiscoveryMetric Learning | CodeCode Available | 1 |
| Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework | Dec 1, 2022 | Drug DiscoveryNER | CodeCode Available | 1 |
| Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation | Apr 23, 2024 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| Accelerating high-throughput virtual screening through molecular pool-based active learning | Dec 13, 2020 | Active LearningBayesian Optimization | CodeCode Available | 1 |
| Activity Cliff Prediction: Dataset and Benchmark | Feb 15, 2023 | Drug DiscoveryPrediction | CodeCode Available | 1 |
| DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening | Oct 10, 2023 | Contrastive LearningData Augmentation | CodeCode Available | 1 |
| Large-Scale Chemical Language Representations Capture Molecular Structure and Properties | Jun 17, 2021 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms | Dec 23, 2023 | Drug 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 |
| EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures | May 20, 2022 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| DrugAssist: A Large Language Model for Molecule Optimization | Dec 28, 2023 | Drug DiscoveryLanguage Modeling | 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 |
| BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations | Oct 11, 2023 | Drug DiscoveryMolecule Captioning | CodeCode Available | 1 |
| DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback | Nov 20, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Directional Message Passing for Molecular Graphs | Mar 6, 2020 | Drug DiscoveryFormation Energy | CodeCode Available | 1 |
| Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences | Nov 6, 2024 | Drug DiscoveryIn-Context Learning | 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 |
| Discrete-state Continuous-time Diffusion for Graph Generation | May 19, 2024 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Automated 3D Pre-Training for Molecular Property Prediction | Jun 13, 2023 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| Extrapolative Controlled Sequence Generation via Iterative Refinement | Mar 8, 2023 | AttributeDrug 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 |
| Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks | Nov 4, 2022 | Drug Discovery | CodeCode Available | 1 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 |
| An adaptive graph learning method for automated molecular interactions and properties predictions | Jun 23, 2022 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| FlowGNN: A Dataflow Architecture for Real-Time Workload-Agnostic Graph Neural Network Inference | Apr 27, 2022 | CPUDrug Discovery | CodeCode Available | 1 |
| PIGNet2: A Versatile Deep Learning-based Protein-Ligand Interaction Prediction Model for Binding Affinity Scoring and Virtual Screening | Jul 3, 2023 | Data AugmentationDrug Discovery | CodeCode Available | 1 |
| Fractional Denoising for 3D Molecular Pre-training | Jul 20, 2023 | DenoisingDrug Discovery | CodeCode Available | 1 |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Dec 4, 2024 | Contrastive LearningDrug Discovery | CodeCode Available | 1 |
| Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation | Nov 5, 2023 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| Accurate ADMET Prediction with XGBoost | Apr 15, 2022 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| GeneDisco: A Benchmark for Experimental Design in Drug Discovery | Oct 22, 2021 | Active LearningDrug Discovery | CodeCode Available | 1 |
| DOCKSTRING: easy molecular docking yields better benchmarks for ligand design | Oct 29, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models | Oct 28, 2021 | Deep LearningDrug Discovery | CodeCode Available | 1 |
| DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery | May 20, 2025 | Drug Discovery | CodeCode Available | 1 |
| DeepGG: a Deep Graph Generator | Jun 7, 2020 | Drug DiscoveryGraph Embedding | CodeCode Available | 1 |
| A Bayesian Model of Dose-Response for Cancer Drug Studies | Jun 10, 2019 | DenoisingDrug 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 |
| Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity | Jan 18, 2022 | Drug Discovery | 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 |
| Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design | Jul 16, 2024 | Drug DiscoveryOut-of-Distribution Generalization | 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 |
| Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction | May 4, 2024 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
