| Robust deep learning based protein sequence design using ProteinMPNN | Jun 4, 2022 | Deep LearningDrug Discovery | CodeCode Available | 3 |
| Highly accurate protein structure prediction with AlphaFold | Jul 15, 2021 | PredictionProtein Folding | CodeCode Available | 3 |
| ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation | Feb 20, 2025 | 3D Molecule GenerationProtein Design | CodeCode Available | 2 |
| Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling | Oct 10, 2024 | Protein Folding | CodeCode Available | 2 |
| Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges | Apr 27, 2021 | Deep LearningProtein Folding | CodeCode Available | 2 |
| PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL | Feb 1, 2025 | PredictionProtein Folding | 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 |
| MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models | Jun 24, 2025 | GPUProtein Folding | CodeCode Available | 2 |
| PS4: a Next-Generation Dataset for Protein Single Sequence Secondary Structure Prediction | Mar 1, 2023 | PredictionProtein Folding | CodeCode Available | 1 |
| Probably Approximately Correct Labels | Jun 12, 2025 | Protein Foldingtext annotation | CodeCode Available | 1 |
| Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures | Jul 13, 2020 | Protein Folding | CodeCode Available | 1 |
| Protein Language Models and Structure Prediction: Connection and Progression | Nov 30, 2022 | Drug DesignLanguage Modelling | CodeCode Available | 1 |
| Rethinking Neural Operations for Diverse Tasks | Mar 29, 2021 | AutoMLImage Classification | CodeCode Available | 1 |
| Progressive Multi-Modality Learning for Inverse Protein Folding | Dec 11, 2023 | cross-modal alignmentData Augmentation | CodeCode Available | 1 |
| Mask prior-guided denoising diffusion improves inverse protein folding | Dec 10, 2024 | DenoisingProtein Folding | CodeCode Available | 1 |
| ParaFold: Paralleling AlphaFold for Large-Scale Predictions | Nov 11, 2021 | CPUGPU | CodeCode Available | 1 |
| Efficient Architecture Search for Diverse Tasks | Apr 15, 2022 | AutoMLNeural Architecture Search | CodeCode Available | 1 |
| AlphaFold Distillation for Protein Design | Oct 5, 2022 | DiversityDrug Discovery | CodeCode Available | 1 |
| Graph Denoising Diffusion for Inverse Protein Folding | Jun 29, 2023 | DenoisingProtein Folding | CodeCode Available | 1 |
| Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation | Jun 2, 2023 | Language ModelingLanguage Modelling | CodeCode Available | 1 |
| AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB | Feb 1, 2022 | DecoderProtein Design | CodeCode Available | 1 |
| Mega-scale experimental analysis of protein folding stability in biology and design | Jul 19, 2023 | Protein FoldingProtein Stability Prediction | CodeCode Available | 1 |
| Bridge-IF: Learning Inverse Protein Folding with Markov Bridges | Nov 4, 2024 | Protein DesignProtein Folding | CodeCode Available | 1 |
| PolyFold: an interactive visual simulator for distance-based protein folding | Feb 14, 2020 | Protein FoldingProtein Structure Prediction | CodeCode Available | 1 |
| Pareto Dominance Archive and Coordinated Selection Strategy-Based Many-Objective Optimizer for Protein Structure Prediction | Feb 22, 2023 | Evolutionary AlgorithmsProtein Folding | CodeCode Available | 1 |
