| 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 |
| 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 |
| 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 |
| PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding | Jun 5, 2022 | Feature EngineeringMulti-Task Learning | 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 |
| ExplainableFold: Understanding AlphaFold Prediction with Explainable AI | Jan 27, 2023 | counterfactualPrediction | 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 |
| Protein Language Models and Structure Prediction: Connection and Progression | Nov 30, 2022 | Drug DesignLanguage Modelling | 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 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | 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 |
| FoldMark: Protecting Protein Generative Models with Watermarking | Oct 27, 2024 | Drug DiscoveryProtein Structure Prediction | CodeCode Available | 1 | 5 |
| CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning | May 14, 2023 | Protein 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 |
| PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design | Nov 30, 2023 | Protein DesignProtein Structure Prediction | CodeCode Available | 0 | 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 |
| pLDDT-Predictor: High-speed Protein Screening Using Transformer and ESM2 | Oct 11, 2024 | Computational EfficiencyProtein 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 |
