| AbDiffuser: full-atom generation of in vitro functioning antibodies | 2023/2024 | Preprint | 10.48550/arXiv.2308.05027 | AbDiffuser |
| AlphaProteo generates novel proteins for biology and health | 2024 | Preprint Technical report | 10.48550/arXiv.2409.08022 | AlphaProteo |
| AntiFold: improved structure-based antibody design using inverse folding | 2025 | Peer-reviewed | 10.1093/bioadv/vbae202 | AntiFold |
| BindCraft: one-shot design of functional protein binders | 2025 | Peer-reviewed | 10.1038/s41586-025-09429-6 | BindCraft |
| BoltzGen: universal binder design | 2025 | Preprint | 10.1101/2025.11.20.689494 | BoltzGen |
| Illuminating protein space with a programmable generative model | 2023 | Peer-reviewed | 10.1038/s41586-023-06728-8 | Chroma |
| Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures | 2022 | NeurIPS 2022 main track (A*) | NR | DiffAb |
| End-to-End Full-Atom Antibody Design | 2023 | ICML 2023 main track (A*) | NR | dyMEAN |
| Efficient evolution of human antibodies from general protein language models | 2024 | Peer-reviewed | 10.1038/s41587-023-01763-2 | Efficient evolution with ESM-1v |
| Learning inverse folding from millions of predicted structures | 2022 | ICML 2022 main track (A*) | 10.48550/arXiv.2204.07148 | ESM-IF1 |
| Simulating 500 million years of evolution with a language model | 2025 | Peer-reviewed | 10.1126/science.ads0018 | ESM3 |
| Protein generation with evolutionary diffusion: sequence is all you need | 2023/2024 | Preprint | 10.1101/2023.09.11.556673 | EvoDiff |
| Few-shot learning for protein evolution with EVOLVEpro | 2025 | Peer-reviewed | 10.1126/science.adr6006 | EVOLVEpro |
| Flow matching for antibody CDR sequence–structure co-design | 2025 | Peer-reviewed | 10.1016/j.cels.2025.101270 | FlowDesign |
| SE(3) diffusion model with application to protein backbone generation | 2023 | ICML 2023 main track (A*) | NR | FrameDiff |
| HuAbDiffusion: humanized antibody generation from CDRs | 2025 | Peer-reviewed | 10.1093/bib/bbaf658 | HuAbDiffusion |
| Humanization of antibodies and nanobodies by diffusion models | 2024/2025 | Preprint | 10.1101/2024.10.22.619416 | HuDiff |
| Humatch: fast and accurate antibody humanization | 2024 | Peer-reviewed | 10.1080/19420862.2024.2434121 | Humatch |
| IgLM: Infilling language modeling for antibody sequence design | 2023 | Peer-reviewed | 10.1016/j.cels.2023.10.001 | IgLM |
| Atomic context-conditioned protein sequence design using LigandMPNN | 2025 | Peer-reviewed | 10.1038/s41592-025-02626-1 | LigandMPNN |
| Co-optimization of therapeutic antibody affinity and specificity using machine learning models of sequence-activity data | 2022 | Peer-reviewed | 10.1038/s41467-022-31457-3 | Makowski et al. affinity–specificity co-optimization |
| xTrimoPGLM-based antigen-specific antibody CDR-H3 design (PALM-H3) | 2024 | Peer-reviewed | 10.1038/s41467-024-50903-y | PALM-H3 |
| Large language models generate functional protein sequences across diverse families | 2023 | Peer-reviewed | 10.1038/s41587-022-01618-2 | ProGen / ProGen2 |
| Generalized biomolecular modeling and design with sequence-space diffusion | 2025 | Peer-reviewed | 10.1038/s41587-024-02395-w | ProteinGenerator |
| Robust deep learning-based protein sequence design using ProteinMPNN | 2022 | Peer-reviewed | 10.1126/science.add2187 | ProteinMPNN |
| Atomically accurate de novo design of antibodies with RFantibody | 2025/2026 | Peer-reviewed | 10.1038/s41586-025-09721-5 | RFantibody |
| Generalized biomolecular modeling and design with RoseTTAFold All-Atom | 2024 | Peer-reviewed | 10.1126/science.adl2528 | RFdiffusion All-Atom (RFdiffusionAA) |
| De novo design of protein structure and function with RFdiffusion | 2023 | Peer-reviewed | 10.1038/s41586-023-06415-8 | RFdiffusion |
| Unsupervised evolution of protein and antibody complexes with a structure-informed language model | 2024 | Peer-reviewed | 10.1126/science.adk8946 | Structural evolution (ESM-IF1 complex) |
| tFold: epitope-specific de novo antibody design | 2025/2026 | Peer-reviewed | 10.1038/s41467-025-67361-9 | tFold System |