| Robust deep learning based protein sequence design using ProteinMPNN | Jun 4, 2022 | Deep LearningDrug Discovery | CodeCode Available | 3 | 5 |
| Highly accurate protein structure prediction with AlphaFold | Jul 15, 2021 | PredictionProtein Folding | CodeCode Available | 3 | 5 |
| State-specific protein-ligand complex structure prediction with a multi-scale deep generative model | Sep 30, 2022 | BenchmarkingBlind Docking | CodeCode Available | 2 | 5 |
| Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling | Oct 10, 2024 | Protein Folding | CodeCode Available | 2 | 5 |
| MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models | Jun 24, 2025 | GPUProtein Folding | CodeCode Available | 2 | 5 |
| PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL | Feb 1, 2025 | PredictionProtein Folding | CodeCode Available | 2 | 5 |
| Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges | Apr 27, 2021 | Deep LearningProtein Folding | CodeCode Available | 2 | 5 |
| ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation | Feb 20, 2025 | 3D Molecule GenerationProtein Design | CodeCode Available | 2 | 5 |
| Towards Expert-Level Medical Question Answering with Large Language Models | May 16, 2023 | Medical Question AnsweringMedQA | CodeCode Available | 1 | 5 |
| Bridge-IF: Learning Inverse Protein Folding with Markov Bridges | Nov 4, 2024 | Protein DesignProtein Folding | CodeCode Available | 1 | 5 |
| TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering | Aug 27, 2024 | Multiple-choiceProtein Folding | CodeCode Available | 1 | 5 |
| Rethinking Neural Operations for Diverse Tasks | Mar 29, 2021 | AutoMLImage Classification | CodeCode Available | 1 | 5 |
| Solvent: A Framework for Protein Folding | Jul 7, 2023 | object-detectionObject Detection | CodeCode Available | 1 | 5 |
| TorchMD: A deep learning framework for molecular simulations | Dec 22, 2020 | BIG-bench Machine LearningDeep Learning | CodeCode Available | 1 | 5 |
| Graph Denoising Diffusion for Inverse Protein Folding | Jun 29, 2023 | DenoisingProtein Folding | CodeCode Available | 1 | 5 |
| Probably Approximately Correct Labels | Jun 12, 2025 | Protein Foldingtext annotation | CodeCode Available | 1 | 5 |
| Protein Language Models and Structure Prediction: Connection and Progression | Nov 30, 2022 | Drug DesignLanguage Modelling | CodeCode Available | 1 | 5 |
| Mask prior-guided denoising diffusion improves inverse protein folding | Dec 10, 2024 | DenoisingProtein Folding | CodeCode Available | 1 | 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 |
| Mega-scale experimental analysis of protein folding stability in biology and design | Jul 19, 2023 | Protein FoldingProtein Stability Prediction | CodeCode Available | 1 | 5 |
| AlphaFold Distillation for Protein Design | Oct 5, 2022 | DiversityDrug Discovery | 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 |
| Progressive Multi-Modality Learning for Inverse Protein Folding | Dec 11, 2023 | cross-modal alignmentData Augmentation | CodeCode Available | 1 | 5 |
| Efficient Architecture Search for Diverse Tasks | Apr 15, 2022 | AutoMLNeural Architecture Search | CodeCode Available | 1 | 5 |
| Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures | Jul 13, 2020 | Protein Folding | 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 |
| AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB | Feb 1, 2022 | DecoderProtein Design | CodeCode Available | 1 | 5 |
| PS4: a Next-Generation Dataset for Protein Single Sequence Secondary Structure Prediction | Mar 1, 2023 | PredictionProtein Folding | CodeCode Available | 1 | 5 |
| ParaFold: Paralleling AlphaFold for Large-Scale Predictions | Nov 11, 2021 | CPUGPU | CodeCode Available | 1 | 5 |
| TG-GAN: Continuous-time Temporal Graph Generation with Deep Generative Models | May 17, 2020 | AttributeGenerative Adversarial Network | CodeCode Available | 0 | 5 |
| Reinforcement Learning for Molecular Dynamics Optimization: A Stochastic Pontryagin Maximum Principle Approach | Dec 6, 2022 | Decision MakingDrug Discovery | CodeCode Available | 0 | 5 |
| Clustering for Protein Representation Learning | Mar 30, 2024 | ClusteringProtein Folding | CodeCode Available | 0 | 5 |
| Simultaneous Coherent Structure Coloring facilitates interpretable clustering of scientific data by amplifying dissimilarity | Jul 12, 2018 | ClusteringProtein Folding | CodeCode Available | 0 | 5 |
| TorchProteinLibrary: A computationally efficient, differentiable representation of protein structure | Nov 23, 2018 | Protein FoldingReinforcement Learning (RL) | CodeCode Available | 0 | 5 |
| Reassessing the Exon-Foldon correspondence using Frustration Analysis | Jan 4, 2024 | Protein Folding | CodeCode Available | 0 | 5 |
| A fast and simple modification of Newton's method helping to avoid saddle points | Jun 2, 2020 | Protein FoldingStochastic Optimization | CodeCode Available | 0 | 5 |
| QFold: Quantum Walks and Deep Learning to Solve Protein Folding | Jan 25, 2021 | Deep LearningProtein Folding | CodeCode Available | 0 | 5 |
| DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations | Jan 24, 2022 | BenchmarkingDrug Discovery | CodeCode Available | 0 | 5 |
| A Study of Acquisition Functions for Medical Imaging Deep Active Learning | Jan 28, 2024 | Active LearningBreast Cancer Detection | CodeCode Available | 0 | 5 |
| Disentangled Dynamic Graph Deep Generation | Oct 14, 2020 | Graph GenerationProtein Folding | CodeCode Available | 0 | 5 |
| Message Scheduling for Performant, Many-Core Belief Propagation | Sep 24, 2019 | GPUProtein Folding | CodeCode Available | 0 | 5 |
| GraphQA: Protein Model Quality Assessment using Graph Convolutional Network | Sep 25, 2019 | Computational EfficiencyProtein Folding | 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 |
| A Parallel Trajectory Swapping Wang - Landau Study Of The HP Protein Model | Jul 12, 2016 | Protein Folding | CodeCode Available | 0 | 5 |
| Learning Collective Variables with Synthetic Data Augmentation through Physics-Inspired Geodesic Interpolation | Feb 2, 2024 | Data AugmentationProtein Folding | CodeCode Available | 0 | 5 |
| DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding | Sep 17, 2019 | Deep LearningProtein Folding | CodeCode Available | 0 | 5 |
| Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model | Sep 2, 2016 | PredictionProtein Folding | CodeCode Available | 0 | 5 |
| Geometric constraints in protein folding | Dec 23, 2018 | Protein Folding | CodeCode Available | 0 | 5 |
| Generative Models for Graph-Based Protein Design | Dec 1, 2019 | Protein DesignProtein Folding | CodeCode Available | 0 | 5 |
| Machine learning in and out of equilibrium | Jun 6, 2023 | NavigateProtein Folding | CodeCode Available | 0 | 5 |
