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| MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models | Jun 24, 2025 | GPUProtein Folding | CodeCode Available | 2 |
| 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 |
| Unfolding AlphaFold's Bayesian Roots in Probability Kinematics | May 26, 2025 | Probabilistic Deep LearningProtein Structure Prediction | —Unverified | 0 |
| Transformers in Protein: A Survey | May 26, 2025 | BenchmarkingDrug Discovery | —Unverified | 0 |
| PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models | May 13, 2025 | Drug DiscoveryProtein Design | CodeCode Available | 0 |
| LightNobel: Improving Sequence Length Limitation in Protein Structure Prediction Model via Adaptive Activation Quantization | May 9, 2025 | Protein FoldingProtein Structure Prediction | —Unverified | 0 |
| AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy | May 6, 2025 | Drug DiscoveryProtein Structure Prediction | —Unverified | 0 |
| Cognitio Emergens: Agency, Dimensions, and Dynamics in Human-AI Knowledge Co-Creation | May 6, 2025 | Protein Structure Prediction | —Unverified | 0 |
| Exploring zero-shot structure-based protein fitness prediction | Apr 23, 2025 | PredictionProtein Structure Prediction | —Unverified | 0 |
| From sequence to protein structure and conformational dynamics with AI/ML | Apr 18, 2025 | Protein Structure Prediction | —Unverified | 0 |
| AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification | Apr 15, 2025 | Drug DiscoveryGraph Neural Network | —Unverified | 0 |
| PETIMOT: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks | Mar 19, 2025 | Graph Neural NetworkProtein Structure Prediction | —Unverified | 0 |
| Advanced Deep Learning Methods for Protein Structure Prediction and Design | Mar 14, 2025 | Deep LearningMultiple Sequence Alignment | —Unverified | 0 |
| Towards Interpretable Protein Structure Prediction with Sparse Autoencoders | Mar 11, 2025 | PredictionProtein Structure Prediction | CodeCode Available | 1 |
| Non-Canonical Crosslinks Confound Evolutionary Protein Structure Models | Mar 9, 2025 | Protein Structure Prediction | —Unverified | 0 |
| Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2 | Feb 28, 2025 | Drug DesignProtein Structure Prediction | —Unverified | 0 |
| A Model-Centric Review of Deep Learning for Protein Design | Feb 26, 2025 | Deep LearningProtein Design | —Unverified | 0 |
| Protein Large Language Models: A Comprehensive Survey | Feb 21, 2025 | ArticlesProtein Structure Prediction | CodeCode Available | 2 |
| MotifBench: A standardized protein design benchmark for motif-scaffolding problems | Feb 18, 2025 | Protein DesignProtein Structure Prediction | CodeCode Available | 2 |
| Deep Learning of Proteins with Local and Global Regions of Disorder | Feb 17, 2025 | Protein Structure Prediction | CodeCode Available | 1 |
| PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL | Feb 1, 2025 | PredictionProtein Folding | CodeCode Available | 2 |
| CENTS: Generating synthetic electricity consumption time series for rare and unseen scenarios | Jan 24, 2025 | Protein Structure PredictionTime Series | —Unverified | 0 |
