| Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction | May 20, 2024 | Drug DesignMolecular Docking | CodeCode Available | 5 | 5 |
| DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking | Oct 4, 2022 | Blind DockingDrug Design | CodeCode Available | 3 | 5 |
| ACEGEN: Reinforcement learning of generative chemical agents for drug discovery | May 7, 2024 | BenchmarkingDecision Making | CodeCode Available | 3 | 5 |
| Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation | May 30, 2024 | DiversityDrug Design | CodeCode Available | 3 | 5 |
| CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph | Jun 16, 2024 | Drug DesignFairness | CodeCode Available | 3 | 5 |
| Test-Time Training Scaling Laws for Chemical Exploration in Drug Design | Jan 31, 2025 | Drug DesignDrug Discovery | CodeCode Available | 3 | 5 |
| Hopfield Networks is All You Need | Jul 16, 2020 | AllDrug Design | CodeCode Available | 2 | 5 |
| Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets | May 15, 2022 | Drug DesignGraph Neural Network | CodeCode Available | 2 | 5 |
| A 3D Generative Model for Structure-Based Drug Design | Mar 20, 2022 | Drug Designvalid | CodeCode Available | 2 | 5 |
| Multi-Objective Molecule Generation using Interpretable Substructures | Feb 8, 2020 | DiversityDrug Design | CodeCode Available | 2 | 5 |
| Generative Flows on Synthetic Pathway for Drug Design | Oct 6, 2024 | Drug DesignDrug Discovery | CodeCode Available | 2 | 5 |
| Efficient Evolutionary Search Over Chemical Space with Large Language Models | Jun 23, 2024 | Drug DesignEvolutionary Algorithms | CodeCode Available | 2 | 5 |
| Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks | Nov 20, 2024 | Bayesian InferenceDrug Design | CodeCode Available | 2 | 5 |
| Mamba-360: Survey of State Space Models as Transformer Alternative for Long Sequence Modelling: Methods, Applications, and Challenges | Apr 24, 2024 | Drug DesignInductive Bias | CodeCode Available | 2 | 5 |
| Compositional Flows for 3D Molecule and Synthesis Pathway Co-design | Apr 10, 2025 | Drug Design | CodeCode Available | 2 | 5 |
| PPFlow: Target-aware Peptide Design with Torsional Flow Matching | Mar 5, 2024 | Drug DesignDrug Discovery | CodeCode Available | 2 | 5 |
| 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction | Mar 6, 2023 | Drug Design | CodeCode Available | 2 | 5 |
| Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule | May 12, 2025 | Drug DesignScheduling | CodeCode Available | 2 | 5 |
| SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints | May 2, 2024 | DiversityDrug Design | CodeCode Available | 2 | 5 |
| A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation | Feb 13, 2024 | Drug Design | CodeCode Available | 2 | 5 |
| Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration | May 30, 2023 | Drug Design | CodeCode Available | 2 | 5 |
| Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond | Jul 13, 2023 | Drug DesignDrug Discovery | CodeCode Available | 2 | 5 |
| Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing | Dec 21, 2022 | Contrastive LearningDrug Design | CodeCode Available | 2 | 5 |
| DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design | Feb 26, 2024 | AvgDrug Design | CodeCode Available | 2 | 5 |
| M^3-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery | Dec 8, 2024 | Drug DesignMolecular Property Prediction | CodeCode Available | 2 | 5 |
| Structure-based Drug Design with Equivariant Diffusion Models | Oct 24, 2022 | Drug DesignSpecificity | CodeCode Available | 2 | 5 |
| NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models | Dec 14, 2024 | BenchmarkingDrug Design | CodeCode Available | 2 | 5 |
| SILVR: Guided Diffusion for Molecule Generation | Apr 21, 2023 | Drug Design | CodeCode Available | 2 | 5 |
| A Systematic Survey of Chemical Pre-trained Models | Oct 29, 2022 | Drug Designmolecular representation | CodeCode Available | 2 | 5 |
| MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space | Apr 18, 2024 | Drug Design | CodeCode Available | 2 | 5 |
| FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction | Jun 3, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design | Jun 24, 2024 | BenchmarkingDrug Design | CodeCode Available | 1 | 5 |
| 3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery | Feb 7, 2025 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations | Nov 9, 2019 | Deep LearningDrug 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 |
| Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks | Jan 5, 2017 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization | Jul 1, 2024 | AvgDrug Design | CodeCode Available | 1 | 5 |
| Accurate Pocket Identification for Binding-Site-Agnostic Docking | Feb 4, 2025 | Blind DockingDrug Design | CodeCode Available | 1 | 5 |
| DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks | Aug 10, 2021 | Drug Design | CodeCode Available | 1 | 5 |
| Evening the Score: Targeting SARS-CoV-2 Protease Inhibition in Graph Generative Models for Therapeutic Candidates | May 7, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories | Jun 19, 2020 | Drug Design | CodeCode Available | 1 | 5 |
| De novo Drug Design using Reinforcement Learning with Multiple GPT Agents | Dec 21, 2023 | DiversityDrug Design | CodeCode Available | 1 | 5 |
| Exploiting Pretrained Biochemical Language Models for Targeted Drug Design | Sep 2, 2022 | Drug Design | CodeCode Available | 1 | 5 |
| Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure | Nov 22, 2023 | Drug Design | CodeCode Available | 1 | 5 |
| Geometric Deep Learning for Structure-Based Drug Design: A Survey | Jun 20, 2023 | BenchmarkingDeep Learning | CodeCode Available | 1 | 5 |
| A fully differentiable ligand pose optimization framework guided by deep learning and traditional scoring functions | Jun 27, 2022 | Drug Design | CodeCode Available | 1 | 5 |
| CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction | Aug 21, 2024 | Drug DesignPrediction | CodeCode Available | 1 | 5 |
| A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences | Jun 7, 2024 | Bayesian OptimizationDrug Design | CodeCode Available | 1 | 5 |
| 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design | May 15, 2022 | Drug Design | CodeCode Available | 1 | 5 |
| Assigning Confidence to Molecular Property Prediction | Feb 23, 2021 | Drug DesignMolecular Docking | CodeCode Available | 1 | 5 |
