| Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop | Jun 22, 2023 | Computational EfficiencyDrug Design | CodeCode Available | 1 |
| Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation | Jun 2, 2023 | Language ModelingLanguage Modelling | CodeCode Available | 1 |
| DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing | Jun 1, 2023 | DenoisingProtein Structure Prediction | CodeCode Available | 1 |
| CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning | May 14, 2023 | Protein Structure Prediction | CodeCode Available | 1 |
| EigenFold: Generative Protein Structure Prediction with Diffusion Models | Apr 5, 2023 | PredictionProtein 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 |
| Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds | Jan 29, 2023 | DenoisingProtein Design | CodeCode Available | 1 |
| ExplainableFold: Understanding AlphaFold Prediction with Explainable AI | Jan 27, 2023 | counterfactualPrediction | CodeCode Available | 1 |
| RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design | Jan 25, 2023 | Contrastive LearningProtein Design | CodeCode Available | 1 |
| Protein Language Models and Structure Prediction: Connection and Progression | Nov 30, 2022 | Drug DesignLanguage Modelling | CodeCode Available | 1 |
| Geometry-Complete Perceptron Networks for 3D Molecular Graphs | Nov 4, 2022 | Graph Neural NetworkGraph Representation Learning | CodeCode Available | 1 |
| A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps | Sep 30, 2022 | Graph Neural NetworkProtein Structure Prediction | CodeCode Available | 1 |
| PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding | Jun 5, 2022 | Feature EngineeringMulti-Task Learning | CodeCode Available | 1 |
| Generative De Novo Protein Design with Global Context | Apr 21, 2022 | Protein DesignProtein Structure Prediction | CodeCode Available | 1 |
| Iterative SE(3)-Transformers | Feb 26, 2021 | Protein Structure Prediction | CodeCode Available | 1 |
| SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning | Oct 16, 2020 | AllBIG-bench Machine Learning | CodeCode Available | 1 |
| Energy-based models for atomic-resolution protein conformations | Apr 27, 2020 | Protein DesignProtein Structure Prediction | CodeCode Available | 1 |
| PolyFold: an interactive visual simulator for distance-based protein folding | Feb 14, 2020 | Protein FoldingProtein Structure Prediction | CodeCode Available | 1 |
| Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations | Nov 9, 2019 | Deep LearningDrug Design | CodeCode Available | 1 |
| ProteinNet: a standardized data set for machine learning of protein structure | Feb 1, 2019 | BIG-bench Machine LearningProtein Secondary Structure Prediction | CodeCode Available | 1 |
| Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion | Jun 17, 2025 | Drug DesignDrug Discovery | —Unverified | 0 |
| Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data | Jun 4, 2025 | DiversityPrediction | —Unverified | 0 |
| Aligning Protein Conformation Ensemble Generation with Physical Feedback | May 30, 2025 | DenoisingDrug Discovery | —Unverified | 0 |
| Transformers in Protein: A Survey | May 26, 2025 | BenchmarkingDrug Discovery | —Unverified | 0 |
| Unfolding AlphaFold's Bayesian Roots in Probability Kinematics | May 26, 2025 | Probabilistic Deep LearningProtein Structure Prediction | —Unverified | 0 |
