| Robust deep learning based protein sequence design using ProteinMPNN | Jun 4, 2022 | Deep LearningDrug Discovery | CodeCode Available | 3 |
| Highly accurate protein structure prediction with AlphaFold | Jul 15, 2021 | PredictionProtein Folding | CodeCode Available | 3 |
| MegaFold: System-Level Optimizations for Accelerating Protein Structure Prediction Models | Jun 24, 2025 | GPUProtein Folding | CodeCode Available | 2 |
| ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation | Feb 20, 2025 | 3D Molecule GenerationProtein Design | CodeCode Available | 2 |
| PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL | Feb 1, 2025 | PredictionProtein Folding | CodeCode Available | 2 |
| Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling | Oct 10, 2024 | Protein Folding | CodeCode Available | 2 |
| State-specific protein-ligand complex structure prediction with a multi-scale deep generative model | Sep 30, 2022 | BenchmarkingBlind Docking | CodeCode Available | 2 |
| Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges | Apr 27, 2021 | Deep LearningProtein Folding | CodeCode Available | 2 |
| Probably Approximately Correct Labels | Jun 12, 2025 | Protein Foldingtext annotation | CodeCode Available | 1 |
| Mask prior-guided denoising diffusion improves inverse protein folding | Dec 10, 2024 | DenoisingProtein Folding | CodeCode Available | 1 |
| Bridge-IF: Learning Inverse Protein Folding with Markov Bridges | Nov 4, 2024 | Protein DesignProtein Folding | CodeCode Available | 1 |
| 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 |
| Progressive Multi-Modality Learning for Inverse Protein Folding | Dec 11, 2023 | cross-modal alignmentData Augmentation | CodeCode Available | 1 |
| Mega-scale experimental analysis of protein folding stability in biology and design | Jul 19, 2023 | Protein FoldingProtein Stability Prediction | CodeCode Available | 1 |
| Solvent: A Framework for Protein Folding | Jul 7, 2023 | object-detectionObject Detection | CodeCode Available | 1 |
| Graph Denoising Diffusion for Inverse Protein Folding | Jun 29, 2023 | DenoisingProtein Folding | CodeCode Available | 1 |
| Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation | Jun 2, 2023 | Language ModelingLanguage Modelling | CodeCode Available | 1 |
| Towards Expert-Level Medical Question Answering with Large Language Models | May 16, 2023 | Medical Question AnsweringMedQA | CodeCode Available | 1 |
| PS4: a Next-Generation Dataset for Protein Single Sequence Secondary Structure Prediction | Mar 1, 2023 | PredictionProtein Folding | 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 |
| Protein Language Models and Structure Prediction: Connection and Progression | Nov 30, 2022 | Drug DesignLanguage Modelling | CodeCode Available | 1 |
| AlphaFold Distillation for Protein Design | Oct 5, 2022 | DiversityDrug Discovery | CodeCode Available | 1 |
| Efficient Architecture Search for Diverse Tasks | Apr 15, 2022 | AutoMLNeural Architecture Search | CodeCode Available | 1 |
| AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB | Feb 1, 2022 | DecoderProtein Design | CodeCode Available | 1 |
| ParaFold: Paralleling AlphaFold for Large-Scale Predictions | Nov 11, 2021 | CPUGPU | CodeCode Available | 1 |
| Rethinking Neural Operations for Diverse Tasks | Mar 29, 2021 | AutoMLImage Classification | CodeCode Available | 1 |
| TorchMD: A deep learning framework for molecular simulations | Dec 22, 2020 | BIG-bench Machine LearningDeep Learning | CodeCode Available | 1 |
| Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures | Jul 13, 2020 | Protein Folding | CodeCode Available | 1 |
| PolyFold: an interactive visual simulator for distance-based protein folding | Feb 14, 2020 | Protein FoldingProtein Structure Prediction | CodeCode Available | 1 |
| Central Dogma Cycle and Network: A Model for Cell Memory | Jun 19, 2025 | Protein Folding | —Unverified | 0 |
| Protein Inverse Folding From Structure Feedback | Jun 3, 2025 | Protein Folding | —Unverified | 0 |
| Protein folding classes -- High-dimensional geometry of amino acid composition space revisited | Jun 2, 2025 | DescriptiveProtein Folding | —Unverified | 0 |
| P: A Universal Measure of Predictive Intelligence | May 30, 2025 | Protein Folding | —Unverified | 0 |
| Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression | May 23, 2025 | Protein Folding | —Unverified | 0 |
| Predicting protein folding dynamics using sequence information | May 22, 2025 | Protein Folding | —Unverified | 0 |
| DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design | May 18, 2025 | Language ModelingLanguage Modelling | —Unverified | 0 |
| LightNobel: Improving Sequence Length Limitation in Protein Structure Prediction Model via Adaptive Activation Quantization | May 9, 2025 | Protein FoldingProtein Structure Prediction | —Unverified | 0 |
| Hallucination, reliability, and the role of generative AI in science | Apr 11, 2025 | HallucinationProtein Folding | —Unverified | 0 |
| Lattice Protein Folding with Variational Annealing | Feb 28, 2025 | Combinatorial OptimizationDrug Design | —Unverified | 0 |
| A Novel P-bit-based Probabilistic Computing Approach for Solving the 3-D Protein Folding Problem | Feb 27, 2025 | Protein Folding | —Unverified | 0 |
| Fluorescence Phasor Analysis: Basic Principles and Biophysical Applications | Feb 14, 2025 | Protein Folding | —Unverified | 0 |
| Inferring protein folding mechanisms from natural sequence diversity | Dec 18, 2024 | DiversityProtein Folding | —Unverified | 0 |
| Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab | Nov 9, 2024 | Protein DesignProtein Folding | —Unverified | 0 |
| Learning dynamical systems from data: Gradient-based dictionary optimization | Nov 7, 2024 | Protein Folding | —Unverified | 0 |
| Generalized Flow Matching for Transition Dynamics Modeling | Oct 19, 2024 | Protein Folding | —Unverified | 0 |
| RapidDock: Unlocking Proteome-scale Molecular Docking | Oct 16, 2024 | Drug DiscoveryGPU | —Unverified | 0 |
| LoRTA: Low Rank Tensor Adaptation of Large Language Models | Oct 5, 2024 | Natural Language Understandingparameter-efficient fine-tuning | —Unverified | 0 |
| Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles | Sep 10, 2024 | Protein Folding | —Unverified | 0 |
| Self-folding Self-replication | Aug 13, 2024 | Protein Folding | —Unverified | 0 |
| Optimal Strategy for Stabilizing Protein Folding Intermediates | Jul 28, 2024 | Protein Folding | —Unverified | 0 |