| Hopfield Networks is All You Need | Jul 16, 2020 | AllDrug Design | CodeCode Available | 2 |
| Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration | May 30, 2023 | Drug Design | CodeCode Available | 2 |
| Compositional Flows for 3D Molecule and Synthesis Pathway Co-design | Apr 10, 2025 | Drug Design | CodeCode Available | 2 |
| MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space | Apr 18, 2024 | Drug Design | CodeCode Available | 2 |
| PPFlow: Target-aware Peptide Design with Torsional Flow Matching | Mar 5, 2024 | Drug DesignDrug Discovery | CodeCode Available | 2 |
| FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction | Jun 3, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design | Jun 24, 2024 | BenchmarkingDrug Design | CodeCode Available | 1 |
| 3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery | Feb 7, 2025 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations | Nov 9, 2019 | Deep LearningDrug Design | CodeCode Available | 1 |
| Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks | Jan 5, 2017 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization | Jul 1, 2024 | AvgDrug Design | CodeCode Available | 1 |
| Accurate Pocket Identification for Binding-Site-Agnostic Docking | Feb 4, 2025 | Blind DockingDrug Design | CodeCode Available | 1 |
| 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 |
| Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design | Oct 6, 2022 | Drug Designvalid | CodeCode Available | 1 |
| 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 |
| Drug–target affinity prediction using graph neural network and contact maps | Jun 1, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| Exploiting Pretrained Biochemical Language Models for Targeted Drug Design | Sep 2, 2022 | Drug Design | CodeCode Available | 1 |
| DiffBindFR: An SE(3) Equivariant Network for Flexible Protein-Ligand Docking | Nov 26, 2023 | Drug DesignMolecular Docking | CodeCode Available | 1 |
| Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure | Nov 22, 2023 | Drug Design | CodeCode Available | 1 |
| Geometric Deep Learning for Structure-Based Drug Design: A Survey | Jun 20, 2023 | BenchmarkingDeep Learning | CodeCode Available | 1 |
| A fully differentiable ligand pose optimization framework guided by deep learning and traditional scoring functions | Jun 27, 2022 | Drug Design | CodeCode Available | 1 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences | Jun 7, 2024 | Bayesian OptimizationDrug Design | CodeCode Available | 1 |
| Endowing Protein Language Models with Structural Knowledge | Jan 26, 2024 | Drug DesignLanguage Modeling | CodeCode Available | 1 |
| 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design | May 15, 2022 | Drug Design | CodeCode Available | 1 |
