| Release Date | Name | Reference | Repository | Model Type | Experimental Validation | Notes |
|---|---|---|---|---|---|---|
| 2022-05-10 | TERMs | Protein Science 31.6 (2022): e4322 | N/A | Scaffold-based | No | |
| 2022-05-24 | Rifdock | Nature 605.7910 (2022): 551 | Github | RifDock + RifGen | Yes | David Baker |
| 2022-07-21 | RFdesign | Science 377.6604 (2022): 387 | Github | Hallucination + Inpainting | Yes | David Baker |
| 2023-02-26 | AfCycDesign | BioRxiv (2023): 2023-02 | Github | AF2-based | Yes | Cyclic Peptide |
| 2023-05-26 | dl-binder-design | Nat. Commun 14.1 (2023): 2625 | Github | Hallucination + Inpainting | Yes | David Baker, Benchmark |
| 2023-06-28 | PepPrCLIP | BioRxiv (2023): 2023-06 | GithubN/A | ESM2 + Diffusion | Yes | |
| 2023-08-08 | Evoplay | Nat. Mach. Intell 5.8 (2023): 845 | Github | RL-based | Yes | |
| 2023-08-26 | AfDesign | IJMS 24.17 (2023): 13257 | Code1, Code2 | AF2-based | No | Cyclic Peptide |
| 2023-09-24 | EvoPro | PNAS 120.49 (2023): e2307371120 | Github | AF2 + ProteinMPNN | Yes | |
| 2023-10-05 | PepMLM | ArXiv:2310.03842 | Github | ESM2-based | Yes | |
| 2023-10-23 | ColabFold + BO | GenBio@NeurIPS2023 Poster | N/A | ColabFold and BO | No | Bayesian Optimization |
| 2023-10-25 | EvoBind | Commun. Chem 6.1 (2023): 229 | Gitlab | Foldseek + ESM-IF1 | Yes | |
| 2024-03-08 | PPFlow | BioRxiv (2024): 2024-03 | N/A | Flow-based | No | PPBench2024 |
| 2024-02-21 | PepGLAD | ArXiv:2402.13555 | N/A | Diffusion-based | No | |
| 2024-03-06 | AMP-Diffusion | BioRxiv (2024): 2024-03 | N/A | ESM2 + Diffusion | No |
| Release Date | Model Name | Reference | Repository | Model Type | Tasks Type |
|---|---|---|---|---|---|
| 2024-02-10 | Scaffold-Lab | BioRxiv (2024): 2024-02 | Github | Benchmark | |
| 2022-07-21 | RFdesign | Science 377.6604 (2022): 387 | Github | AF2-based | Hallucination, Unconditional, Inpainting |
| 2022-06-27 | Ig-VAE | PLoS Comput. Biol 18.6 (2022): e1010271 | Github | VAE-based | Unconditional |
| 2022-07-01 | ProteinSGM | Nat. Comput. Sci 3.5 (2023): 382 | Gitlab | Diffusion-based | Unconditional, Inpainting |
| 2023-01-01 | DiffSDS | ArXiv:2301.09642 | Github | Diffusion-based | Inpainting |
| 2023-01-29 | Genie | ArXiv:2301.12485 | Github | Diffusion-based | Unconditional |
| 2023-02-05 | FrameDiff | ArXiv:2302.02277 | Github | Diffusion-based | Unconditional |
| 2023-05-10 | Protein Generator | BioRxiv (2023): 2023-05 | Github Huggingface | Diffusion-based | Unconditional, Inpainting |
| 2023-05-25 | Protpardelle | BioRxiv (2023): 2023-05 | Github | Diffusion-based | Unconditional, Side-chain conditional |
| 2023-06-11 | RFdiffusion | Nature 620.7976 (2023): 1089 | Github | Diffusion-based | General |
| 2023-06-30 | TDS | ArXiv:2306.17775 | Github | Diffusion-based | Conditional |
| 2023-10-30 | GPDL | BioRxiv (2023): 2023-10 | Github | ESM-based | Conditional |
| 2023-10-08 | FrameFlow | ArXiv:2310.05297 | Github | Flow-based | Unconditional |
| 2023-11-15 | Chroma | Nature 623.7989 (2023): 1070 | Github | Diffusion-based | General |
| 2024–02-28 | PocketGen | BioRxiv (2024) 2024-02 | Github | Bilevel graph transformer | Inpainting |
| 2024–03-07 | RFdiffusion-AA | Science (2024): eadl2528 | Github | Diffusion-based | General |
| Name | Source Type | Affinity Type | Dataset Size | Protein Type | Download Link | Notes |
|---|---|---|---|---|---|---|
| SKEMPI 2.0 | Dataset | ΔΔG/ΔG | 6193/346 | General | Link | |
| ATLAS | Dataset | ΔΔG/ΔG | 604/65 | MHC-TCR | Link | |
| GeoPPI | Paper | ΔΔG | 6538 | General | Link | |
| mmCSM-PPI | Paper | ΔΔG | 1340 | General | Link | SKEMPI 2.0 + etc. |
| TopNetTree | Paper | ΔΔG | 1290 | Antigen-Antibody | Link | AB_Bind + etc. |
| AB_Bind | Dataset | ΔΔG | 1101 | Antigen-Antibody | Link | |
| BindPPI | Paper | ΔG | 1467 | General | Link | |
| NERE | Paper | ΔG | 566 | Antigen-Antibody | Link | From Sabdab |
| Sabdab | Dataset | ΔG | 467 | Antigen-Antibody | Link | |
| CSM-AB | Paper | ΔG | 473 | Antigen-Antibody | Link | From Sabdab |
| AREA-AFFINITY | Paper | ΔG | 297 | Antigen-Antibody | Link | From CSM-ABB |
| LISA | Paper | ΔG | 179 | General | Link | |
| PRO_580 | Paper | ΔG | 144 | General | Link | |
| Prodigy | Paper | ΔG | 81 | General | Link |