| Galactica: A Large Language Model for Science | Nov 16, 2022 | AnachronismsBias Detection | CodeCode Available | 4 | 5 |
| OpenProteinSet: Training data for structural biology at scale | Aug 10, 2023 | Protein DesignProtein Structure Prediction | CodeCode Available | 4 | 5 |
| Highly accurate protein structure prediction with AlphaFold | Jul 15, 2021 | PredictionProtein Folding | CodeCode Available | 3 | 5 |
| Robust deep learning based protein sequence design using ProteinMPNN | Jun 4, 2022 | Deep LearningDrug Discovery | CodeCode Available | 3 | 5 |
| MotifBench: A standardized protein design benchmark for motif-scaffolding problems | Feb 18, 2025 | Protein DesignProtein Structure Prediction | CodeCode Available | 2 | 5 |
| FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours | Mar 2, 2022 | Protein Structure PredictionTranslation | CodeCode Available | 2 | 5 |
| Protein Large Language Models: A Comprehensive Survey | Feb 21, 2025 | ArticlesProtein Structure Prediction | CodeCode Available | 2 | 5 |
| MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models | Jun 24, 2025 | GPUProtein Folding | CodeCode Available | 2 | 5 |
| State-specific protein-ligand complex structure prediction with a multi-scale deep generative model | Sep 30, 2022 | BenchmarkingBlind Docking | CodeCode Available | 2 | 5 |
| SE(3) diffusion model with application to protein backbone generation | Feb 5, 2023 | Protein Structure Prediction | CodeCode Available | 2 | 5 |
| Protein structure generation via folding diffusion | Sep 30, 2022 | DenoisingProtein Structure Prediction | CodeCode Available | 2 | 5 |
| Distribution-Free, Risk-Controlling Prediction Sets | Jan 7, 2021 | BIG-bench Machine LearningClassification | CodeCode Available | 2 | 5 |
| Training on test proteins improves fitness, structure, and function prediction | Nov 4, 2024 | PredictionProtein Structure Prediction | CodeCode Available | 2 | 5 |
| PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL | Feb 1, 2025 | PredictionProtein Folding | CodeCode Available | 2 | 5 |
| ProteinBERT: a universal deep-learning model of protein sequence and function | Feb 10, 2022 | Language ModelingLanguage Modelling | CodeCode Available | 2 | 5 |
| Pareto Dominance Archive and Coordinated Selection Strategy-Based Many-Objective Optimizer for Protein Structure Prediction | Feb 22, 2023 | Evolutionary AlgorithmsProtein Folding | CodeCode Available | 1 | 5 |
| MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training | Jun 8, 2024 | Few-Shot LearningMultiple Sequence Alignment | CodeCode Available | 1 | 5 |
| A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps | Sep 30, 2022 | Graph Neural NetworkProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Towards Interpretable Protein Structure Prediction with Sparse Autoencoders | Mar 11, 2025 | PredictionProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations | Nov 9, 2019 | Deep LearningDrug Design | CodeCode Available | 1 | 5 |
| Iterative SE(3)-Transformers | Feb 26, 2021 | Protein Structure Prediction | CodeCode Available | 1 | 5 |
| RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design | Jan 25, 2023 | Contrastive LearningProtein Design | CodeCode Available | 1 | 5 |
| ProteinNet: a standardized data set for machine learning of protein structure | Feb 1, 2019 | BIG-bench Machine LearningProtein Secondary Structure Prediction | CodeCode Available | 1 | 5 |
| PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding | Jun 5, 2022 | Feature EngineeringMulti-Task Learning | CodeCode Available | 1 | 5 |
| CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning | May 14, 2023 | Protein Structure Prediction | CodeCode Available | 1 | 5 |
| SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning | Oct 16, 2020 | AllBIG-bench Machine Learning | CodeCode Available | 1 | 5 |
| Accurate and efficient protein embedding using multi-teacher distillation learning | May 20, 2024 | PredictionProtein Annotation | CodeCode Available | 1 | 5 |
| Generative diffusion model with inverse renormalization group flows | Jan 15, 2025 | Audio SynthesisDenoising | CodeCode Available | 1 | 5 |
| A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems | Dec 12, 2023 | Protein Structure PredictionSpecificity | CodeCode Available | 1 | 5 |
| Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds | Jan 29, 2023 | DenoisingProtein Design | CodeCode Available | 1 | 5 |
| Protein Language Models and Structure Prediction: Connection and Progression | Nov 30, 2022 | Drug DesignLanguage Modelling | CodeCode Available | 1 | 5 |
| Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop | Jun 22, 2023 | Computational EfficiencyDrug Design | CodeCode Available | 1 | 5 |
| Energy-based models for atomic-resolution protein conformations | Apr 27, 2020 | Protein DesignProtein Structure Prediction | CodeCode Available | 1 | 5 |
| EigenFold: Generative Protein Structure Prediction with Diffusion Models | Apr 5, 2023 | PredictionProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation | Jun 2, 2023 | Language ModelingLanguage Modelling | CodeCode Available | 1 | 5 |
| PolyFold: an interactive visual simulator for distance-based protein folding | Feb 14, 2020 | Protein FoldingProtein Structure Prediction | CodeCode Available | 1 | 5 |
| ExplainableFold: Understanding AlphaFold Prediction with Explainable AI | Jan 27, 2023 | counterfactualPrediction | CodeCode Available | 1 | 5 |
| DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing | Jun 1, 2023 | DenoisingProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Deep Learning of Proteins with Local and Global Regions of Disorder | Feb 17, 2025 | Protein Structure Prediction | CodeCode Available | 1 | 5 |
| AtomSurf : Surface Representation for Learning on Protein Structures | Sep 28, 2023 | Atom3D benchmarkProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins | Jul 11, 2025 | PredictionProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Generative De Novo Protein Design with Global Context | Apr 21, 2022 | Protein DesignProtein Structure Prediction | CodeCode Available | 1 | 5 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 | 5 |
| FoldMark: Protecting Protein Generative Models with Watermarking | Oct 27, 2024 | Drug DiscoveryProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Geometry-Complete Perceptron Networks for 3D Molecular Graphs | Nov 4, 2022 | Graph Neural NetworkGraph Representation Learning | CodeCode Available | 1 | 5 |
| MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction | May 10, 2016 | General Classificationimage-classification | CodeCode Available | 0 | 5 |
| Applying Deep Reinforcement Learning to the HP Model for Protein Structure Prediction | Nov 27, 2022 | Deep Reinforcement LearningProtein Folding | CodeCode Available | 0 | 5 |
| PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design | Nov 30, 2023 | Protein DesignProtein Structure Prediction | CodeCode Available | 0 | 5 |
| MAS2HP: A Multi Agent System to Predict Protein Structure in 2D HP model | May 11, 2022 | Protein Structure Prediction | CodeCode Available | 0 | 5 |
| APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics | Aug 15, 2023 | Drug DiscoveryPrediction | CodeCode Available | 0 | 5 |
