📘 Related paper reading list: Awesome protein structure prediction (PSP) methods
| Title | Pub.&Year | Notes | |
|---|---|---|---|
| AlphaFold2 | Highly accurate protein structure prediction with AlphaFold | Nature '2021 | code |
| ColabFold | ColabFold: making protein folding accessible to all | Nature '2021 | |
| AFM | Protein complex prediction with AlphaFold-Multimer | bioRxiv '2022 | |
| ESMFold (ESM2) | Evolutionary-scale prediction of atomic-level protein structure with a language model | Science '2023 | |
| [Survey] | Protein Language Models and Structure Prediction: Connection and Progression | Arxiv '2022 | |
| [Survey] | Recent Advances and Challenges in Protein Structure Prediction | JCIM' 2023 | |
| AlphaFold3 | Accurate structure prediction of biomolecular interactions with AlphaFold 3 | Nature '2024 | web server |
| Chai | Chai-1 Technical Report | 2024 | code, web server |
| Title | Pub.&Year | Notes | |
|---|---|---|---|
| "Glinker" | Can AlphaFold2 predict protein-peptide complex structures accurately?, Harnessing protein folding neural networks for peptide–protein docking |
bioRxiv' 2021, NC '2022 |
|
| [Benchmark] | Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants | Protein Science' 2022 | |
| [Benchmark] | Predicting Protein–Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking | JCIM' 2022 | |
| [Benchmark] | Evaluation of AlphaFold antibody–antigen modeling with implications for improving predictive accuracy | Protein Science' 2024 | |
| De novo design of high-affinity protein binders with AlphaProteo | Arxiv '2024 |