| OpenProteinSet: Training data for structural biology at scale | Aug 10, 2023 | Protein DesignProtein Structure Prediction | CodeCode Available | 4 |
| Galactica: A Large Language Model for Science | Nov 16, 2022 | AnachronismsBias Detection | CodeCode Available | 4 |
| Highly accurate protein structure prediction with AlphaFold | Jul 15, 2021 | PredictionProtein Folding | CodeCode Available | 3 |
| Robust deep learning based protein sequence design using ProteinMPNN | Jun 4, 2022 | Deep LearningDrug Discovery | CodeCode Available | 3 |
| PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL | Feb 1, 2025 | PredictionProtein Folding | CodeCode Available | 2 |
| Protein Large Language Models: A Comprehensive Survey | Feb 21, 2025 | ArticlesProtein Structure Prediction | CodeCode Available | 2 |
| State-specific protein-ligand complex structure prediction with a multi-scale deep generative model | Sep 30, 2022 | BenchmarkingBlind Docking | CodeCode Available | 2 |
| Protein structure generation via folding diffusion | Sep 30, 2022 | DenoisingProtein Structure Prediction | CodeCode Available | 2 |
| Training on test proteins improves fitness, structure, and function prediction | Nov 4, 2024 | PredictionProtein Structure Prediction | CodeCode Available | 2 |
| SE(3) diffusion model with application to protein backbone generation | Feb 5, 2023 | Protein Structure Prediction | CodeCode Available | 2 |
| MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models | Jun 24, 2025 | GPUProtein Folding | CodeCode Available | 2 |
| FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours | Mar 2, 2022 | Protein Structure PredictionTranslation | CodeCode Available | 2 |
| Distribution-Free, Risk-Controlling Prediction Sets | Jan 7, 2021 | BIG-bench Machine LearningClassification | CodeCode Available | 2 |
| MotifBench: A standardized protein design benchmark for motif-scaffolding problems | Feb 18, 2025 | Protein DesignProtein Structure Prediction | CodeCode Available | 2 |
| ProteinBERT: a universal deep-learning model of protein sequence and function | Feb 10, 2022 | Language ModelingLanguage Modelling | CodeCode Available | 2 |
| RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design | Jan 25, 2023 | Contrastive LearningProtein Design | CodeCode Available | 1 |
| Generative diffusion model with inverse renormalization group flows | Jan 15, 2025 | Audio SynthesisDenoising | CodeCode Available | 1 |
| Geometry-Complete Perceptron Networks for 3D Molecular Graphs | Nov 4, 2022 | Graph Neural NetworkGraph Representation Learning | CodeCode Available | 1 |
| Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds | Jan 29, 2023 | DenoisingProtein Design | CodeCode Available | 1 |
| Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations | Nov 9, 2019 | Deep LearningDrug Design | CodeCode Available | 1 |
| Generative De Novo Protein Design with Global Context | Apr 21, 2022 | Protein DesignProtein Structure Prediction | CodeCode Available | 1 |
| Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop | Jun 22, 2023 | Computational EfficiencyDrug Design | CodeCode Available | 1 |
| Energy-based models for atomic-resolution protein conformations | Apr 27, 2020 | Protein DesignProtein Structure Prediction | CodeCode Available | 1 |
| FoldMark: Protecting Protein Generative Models with Watermarking | Oct 27, 2024 | Drug DiscoveryProtein Structure Prediction | CodeCode Available | 1 |
| Accurate and efficient protein embedding using multi-teacher distillation learning | May 20, 2024 | PredictionProtein Annotation | CodeCode Available | 1 |
