| Endowing Protein Language Models with Structural Knowledge | Jan 26, 2024 | Drug DesignLanguage Modeling | CodeCode Available | 1 | 5 |
| MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights | Dec 21, 2024 | Drug DesignMamba | CodeCode Available | 1 | 5 |
| DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback | Nov 20, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders | Mar 23, 2022 | Bayesian OptimizationDenoising | 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 |
| Molecular Contrastive Learning with Chemical Element Knowledge Graph | Dec 1, 2021 | Contrastive LearningDrug Design | CodeCode Available | 1 | 5 |
| Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design | Oct 6, 2022 | Drug Designvalid | CodeCode Available | 1 | 5 |
| Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spaces | Nov 1, 2021 | Bayesian OptimizationDrug Design | CodeCode Available | 1 | 5 |
| CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions | Jun 26, 2025 | BenchmarkingDrug Design | CodeCode Available | 1 | 5 |
| DOCKSTRING: easy molecular docking yields better benchmarks for ligand design | Oct 29, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design | May 15, 2022 | Drug Design | CodeCode Available | 1 | 5 |
| Domain-Agnostic Molecular Generation with Chemical Feedback | Jan 26, 2023 | Drug DesignLanguage Modeling | CodeCode Available | 1 | 5 |
| Multimodal Large Language Models for Inverse Molecular Design with Retrosynthetic Planning | Oct 5, 2024 | BenchmarkingDrug Design | 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 |
| Geometric Representation Condition Improves Equivariant Molecule Generation | Oct 4, 2024 | Drug Designscientific discovery | CodeCode Available | 1 | 5 |
| Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design | Sep 16, 2024 | DenoisingDrug Design | CodeCode Available | 1 | 5 |
| FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction | Jun 3, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| De novo Drug Design using Reinforcement Learning with Multiple GPT Agents | Dec 21, 2023 | DiversityDrug Design | CodeCode Available | 1 | 5 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Modeling PROTAC Degradation Activity with Machine Learning | Jun 4, 2024 | Binary ClassificationDrug Design | CodeCode Available | 1 | 5 |
| GraphGT: Machine Learning Datasets for Graph Generation and Transformation | Sep 24, 2021 | BIG-bench Machine LearningDrug Design | 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 |
| GraphXForm: Graph transformer for computer-aided molecular design | Nov 3, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop | Jun 22, 2023 | Computational EfficiencyDrug Design | CodeCode Available | 1 | 5 |
| Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning | Apr 26, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
