| Deep Confident Steps to New Pockets: Strategies for Docking Generalization | Feb 28, 2024 | Blind Docking | CodeCode Available | 5 | 5 |
| DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking | Oct 4, 2022 | Blind DockingDrug Design | CodeCode Available | 3 | 5 |
| FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction | Dec 14, 2024 | Blind DockingDrug Discovery | CodeCode Available | 3 | 5 |
| State-specific protein-ligand complex structure prediction with a multi-scale deep generative model | Sep 30, 2022 | BenchmarkingBlind Docking | CodeCode Available | 2 | 5 |
| EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction | Feb 7, 2022 | Blind DockingDeep Learning | 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 |
| 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 |
| Accurate Pocket Identification for Binding-Site-Agnostic Docking | Feb 4, 2025 | Blind DockingDrug Design | 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 |
| FABind: Fast and Accurate Protein-Ligand Binding | Oct 10, 2023 | Blind DockingDrug Discovery | CodeCode Available | 1 | 5 |
| SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation | Feb 26, 2025 | Blind DockingDecoder | CodeCode Available | 1 | 5 |
| GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking | Nov 19, 2024 | Blind DockingDrug Discovery | —Unverified | 0 | 0 |
| Group Ligands Docking to Protein Pockets | Jan 25, 2025 | Blind DockingMolecular Docking | —Unverified | 0 | 0 |
| Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking | Nov 30, 2023 | Blind DockingGPU | —Unverified | 0 | 0 |
| DSDP: A Blind Docking Strategy Accelerated by GPUs | Mar 16, 2023 | Blind DockingDrug Discovery | —Unverified | 0 | 0 |
| Quantum-Inspired Machine Learning for Molecular Docking | Jan 22, 2024 | Blind DockingCombinatorial Optimization | —Unverified | 0 | 0 |
| Seq2Bind Webserver for Decoding Binding Hotspots directly from Sequences using Fine-Tuned Protein Language Models | Jun 16, 2025 | Blind Docking | —Unverified | 0 | 0 |
| GeoDirDock: Guiding Docking Along Geodesic Paths | Apr 9, 2024 | Blind DockingDenoising | —Unverified | 0 | 0 |
