| Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction | May 20, 2024 | Drug DesignMolecular Docking | CodeCode Available | 5 | 5 |
| Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity | Mar 30, 2017 | Drug DiscoveryMolecular Docking | CodeCode Available | 3 | 5 |
| Modeling Molecular Structures with Intrinsic Diffusion Models | Feb 23, 2023 | Computational chemistryMolecular Docking | CodeCode Available | 3 | 5 |
| DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking | Oct 4, 2022 | Blind DockingDrug Design | CodeCode Available | 3 | 5 |
| DisCo-Diff: Enhancing Continuous Diffusion Models with Discrete Latents | Jul 3, 2024 | Image GenerationMolecular Docking | CodeCode Available | 2 | 5 |
| PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning | Jun 24, 2025 | BenchmarkingDrug Discovery | CodeCode Available | 2 | 5 |
| Fast and Accurate Blind Flexible Docking | Feb 20, 2025 | Blind DockingComputational Efficiency | CodeCode Available | 2 | 5 |
| PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking | May 3, 2025 | Blind DockingMolecular Docking | CodeCode Available | 2 | 5 |
| FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation | Mar 29, 2024 | Blind DockingDrug Discovery | CodeCode Available | 2 | 5 |
| QuickBind: A Light-Weight And Interpretable Molecular Docking Model | Oct 21, 2024 | Drug DiscoveryMolecular Docking | CodeCode Available | 1 | 5 |
| CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions | Jun 26, 2025 | BenchmarkingDrug Design | CodeCode Available | 1 | 5 |
| Assigning Confidence to Molecular Property Prediction | Feb 23, 2021 | Drug DesignMolecular Docking | CodeCode Available | 1 | 5 |
| Domain-Agnostic Molecular Generation with Chemical Feedback | Jan 26, 2023 | Drug DesignLanguage Modeling | CodeCode Available | 1 | 5 |
| Protein language models are performant in structure-free virtual screening | Apr 20, 2024 | Drug DesignMolecular Docking | CodeCode Available | 1 | 5 |
| SHREC 2022: Protein-ligand binding site recognition | Jun 13, 2022 | Drug DesignMolecular Docking | CodeCode Available | 1 | 5 |
| PLANTAIN: Diffusion-inspired Pose Score Minimization for Fast and Accurate Molecular Docking | Jul 22, 2023 | BenchmarkingMolecular Docking | CodeCode Available | 1 | 5 |
| DiffBindFR: An SE(3) Equivariant Network for Flexible Protein-Ligand Docking | Nov 26, 2023 | Drug DesignMolecular Docking | CodeCode Available | 1 | 5 |
| CompassDock: Comprehensive Accurate Assessment Approach for Deep Learning-Based Molecular Docking in Inference and Fine-Tuning | Jun 10, 2024 | Molecular Docking | CodeCode Available | 1 | 5 |
| DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking | Oct 15, 2024 | Blind DockingDrug Design | CodeCode Available | 1 | 5 |
| DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries | Nov 30, 2022 | DenoisingMolecular Docking | CodeCode Available | 1 | 5 |
| Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms | Dec 7, 2023 | Molecular Docking | CodeCode Available | 1 | 5 |
| Direct Molecular Conformation Generation | Feb 3, 2022 | Molecular Docking | CodeCode Available | 1 | 5 |
| 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 | 5 |
| DOCKSTRING: easy molecular docking yields better benchmarks for ligand design | Oct 29, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Enhancing Ligand Pose Sampling for Molecular Docking | Nov 30, 2023 | BenchmarkingMolecular Docking | CodeCode Available | 1 | 5 |
