Protein Structure Prediction

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Overview

Protein structure prediction aims to infer how amino-acid sequences form three-dimensional structures, which helps explain protein function and interactions. Approaches range from evolutionary information in multiple-sequence alignments and protein language models to geometric neural networks and generative methods such as diffusion; experimental restraints from cryo-EM or cross-linking can further guide predictions. Evaluation spans structure-accuracy benchmarks such as CAMEO and tests of complexes, binding, and physical plausibility. Models now tackle large assemblies and multiple conformations, but balancing accuracy, inference cost, reliable evaluation, and realistic dynamic behavior remains challenging.

Latest papers

CardsList

40 papers10 papers in the last four weeks, against 1 the four weeks before. 0.1% of all new papers.

  1. Structure, Not Sequence: Tracking and Validating Folding Mechanisms in ESMFold's Trunk with Sparse Autoencoders

    Oct 26, 2026Bohan Liu, Xiaohan Fan, Wenqian Ye +1Protein Structure PredictionNeural Network Interpretability

    University of Virginia Charlottesville VA 22903, USA

  2. Trion-1: Unifying Language, Protein Sequence, and Structure with Diffusion Language Models

    Oct 22, 2026Tianyu Lu, Kaicheng Yang, Jiangtao Feng +7Protein Language ModelsProtein Structure Generation

  3. recAMPLIFY: Large-Scale Pretraining of Recursive Protein Language Models

    Oct 19, 2026Saurav Jha, Qianli Liao, Robert Vernon +2Protein Language ModelsRecursive Language Models

    Mila – Quebec AI Institute · Polytechnique Montréal · Center for Brains, Minds, and Machines +4

  4. Blitz: Accelerating the Diffusion Modules of AlphaFold3 and Boltz-2

    Oct 16, 2026Vinay Saji Mathew, Soundar Kumara, Gretta Kellogg +1Protein Structure PredictionDiffusion Model Inference Acceleration

    Department of Industrial and Manufacturing Engineering, The Pennsylvania State University · Institute for Computational and Data Sciences, The Pennsylvania State University · Department of Biochemistry, University at Buffalo, State University of New York

  5. Refined Topology-Pass Scheduling: Damped Trust-Region Compensation for Dynamic k-NN Graphs in SE(3)-Equivariant Structure Prediction

    Oct 13, 2026Jiankai Huang, Hanwen ShenProtein Structure Predictionk-Nearest Neighbors

  6. Learning from Hetero Density for Cryo-EM Protein Reconstruction

    Oct 8, 2026Xu Han, Chaozhuo Li, Xiaowei Yuan +3Cryo-Electron MicroscopyProtein Structure Prediction

    University of Chinese Academy of Sciences, Beijing, China · Key Laboratory of Complex Systems Cognition and Decision, Institute of Automation, Chinese Academy of Sciences, Beijing, China · Beijing Academy of Artificial Intelligence, Beijing, China +2

  7. A Shortcut to Structure in AlphaFold 3

    Oct 6, 2026Jonathan Feldman, Jeffrey SkolnickProtein Structure PredictionMechanistic Interpretability

    College of Computing, Georgia Institute of Technology, Atlanta, Georgia, USA · Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, Georgia, USA · School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA +1

  8. TurboPairFormer: Fast and Stable Protein Folding Model Training with an Optimized Triangle Attention Kernel

    Oct 5, 2026Yide Ran, Chelsea Lowman, Jan Domański +6Protein Structure PredictionGPU Kernel Optimization

    Stevens Institute of Technology · Lambda · Open Molecular Software Foundation

  9. Inference-Time Projection for Physically Valid Biomolecular Diffusion Models

    Oct 4, 2026Qurat-ul-ain, Yee Whye Teh, Charlotte M. Deane +1Protein Structure Prediction3D Diffusion Models

    Department of Statistics, University of Oxford · Department of Biology, University of Copenhagen

  10. Learning Latent Protein Languages for Autoregressive Generation

    Oct 2, 2026Mahdi Pourmirzaei, Farzaneh Esmaili, Amir Ziashahabi +2Protein Structure GenerationProtein Language Models

    University of Missouri · University of Southern California · Independent Researcher

  11. Does Learning Protein Folding Generalize to Broader Reasoning?

    Sep 30, 2026Yong Liu, Zhanpeng Shi, Yizhou Dang +4Protein Structure PredictionStructured Reasoning

    Shanghai Jiao Tong University · Fudan University · Shanghai Innovation Institute +1

  12. Correcting the Dropout-LayerNorm Expectation Gap Improves Protein Structure Models

    Sep 25, 2026Isaac Ellmen, David Errington, Matthew I. J. Raybould +1Protein Structure PredictionLayer Normalization

    Department of Statistics, University of Oxford · Recursion

  13. AgentFold: Closed-Loop Agentic Search for Protein Folding Model Design

    Aug 27, 2026Mingquan Liu, Jiangyu Chen, Hanqun Cao +9AI Agents for Scientific DiscoveryProtein Structure Prediction

    State Key Lab. of Chemo & Biosensing, Coll. of Comp. Sci. & Electron. Eng., Hunan University · State Key Laboratory for Novel Software Technology, Sch. of Comput. Sci., Nanjing University · The Chinese University of Hong Kong +6

  14. Protein Structure Prediction: From Evolutionary Constraints to Generative Modeling

    Aug 17, 2026Wengan He, Yongsheng Luo, Lihong Jiang +2Protein Structure PredictionProtein Representation Learning

    Zhuhai College of Science and Technology, Zhuhai, China · Zhuhai UNO Technology Co., Ltd., Zhuhai, China

  15. How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models

    Aug 12, 2026Aleksandra Kalisz, Jack Simons, Krisztina Sinkovics +4Protein Structure PredictionInference-Time Optimization

    InstaDeep Ltd · University of Oxford · Lancaster University

  16. Probing and steering biology across Boltz-1s trunk-diffusion boundary

    Aug 11, 2026Piotr Jedryszek, Tongmeng Xie, Adam Winnifrith +5Protein Structure PredictionActivation Steering

    Department of Biology, University of Oxford, Oxford, UK · Evolvere Biosciences, London, UK · Independent Researcher +4

  17. DynaPPI: A Large-scale Dynamic Protein Dataset for AI-driven Advances in Protein Interactomics

    Aug 11, 2026Jiabao Wei, Zilong Geng, Yuze Wang +5Protein Structure PredictionProtein-Protein Interaction Prediction

    1BIT · 3SJTU · 2HUST +2

  18. APO: Unsupervised Atomic Policy Optimization for 3D Structure Prediction of Atomic Systems

    Jul 30, 2026Shentong Mo, Yatao BianProtein Structure PredictionCrystal Structure Prediction

    CMU · NUS

  19. Neural spectroscopy of AlphaFold2 reveals encoded protein conformational landscapes

    Jul 17, 2026Kaustav MehtaProtein Structure PredictionNeural Network Interpretability

    Independent researcher, India

  20. Folding, Reasoning, and Scaling with Open-source Drug Discovery Engine

    Jul 4, 2026Aureka AI OpenDDE projectProtein Structure PredictionMolecular Foundation Models

    OpenDDE Project, Aureka AI Research

  21. CryoACE: An Atom-centric Framework for Accurate and Automated Model Building in Cryo-EM

    Jun 30, 2026Minzhang Li, Mingrui Li, Weichen Qin +5Protein Structure PredictionCryo-Electron Microscopy

    School of Information Science and Technology, ShanghaiTech University, Shanghai, China · Cellverse Co, Ltd., Shanghai, China.

  22. Protein contacts are already in the attention: a single-forward-pass alternative to the Categorical Jacobian

    Jun 20, 2026Rome ThorstensonProtein Structure PredictionAttention Head Analysis

    Independent Researcher

  23. Few-step Cofolding with All-Atom Flow Maps

    Jun 7, 2026Gianluca Scarpellini, Ron Shprints, Peter Holderrieth +7Protein Structure PredictionDiffusion Distillation

    1Genesis Molecular AI · Massachusetts Institute of Technology · Carnegie Mellon University +2

  24. Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

    May 28, 2026Aydin Wells, Francis A. Gatsi, Aaron Striegel +1Protein Structure PredictionGraph Representation Learning

    Department of Computer Science and Engineering, University of Notre Dame, USA

  25. Computational Modeling of Antibody-Antigen Complexes: PLM-Based and MSA-Based Approaches

    May 27, 2026Xiao LuoProtein Structure PredictionAI-Assisted Scientific Research

    TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO, CHICAGO, ILLINOIS

  26. Co-folding model guided by structural proteomics

    May 25, 2026Alon Shtrikman, Nitzan Simchi, Michal Ran Shchory +3Diffusion Model GuidanceProtein Structure Prediction

    1Protai Bio

  27. Atom-level Protein Representation Learning Improves Protein Structure Prediction

    May 21, 2026Taewon Kim, Hyosoon Jang, Hyunjin Seo +6Protein Structure PredictionSelf-Supervised Pre-Training

    Graduate School of AI, KAIST · Department of Chemistry, KAIST · HITS Inc. +3

  28. DCFold: Efficient Protein Structure Generation with Single Forward Pass

    May 18, 2026Zhe Zhang, Yuanning Feng, Yuxuan Song +3Protein Structure PredictionProtein Structure Generation

    Institute for AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · School of Computer Science and Technology, Huazhong University of Science and Technology +1

  29. Deep Learning for Protein Complex Prediction and Design

    May 11, 2026Ziwei XieProtein Structure PredictionMolecular Generation

    TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO, Chicago, Illinois

  30. Modeling Atomic Conformational Ensembles of Proteins via Test-Time Supervision of Boltz-2 on Cryo-EM Density Maps

    May 11, 2026Jay Shenoy, Miro Astore, Axel Levy +3Supervised Fine-TuningProtein Structure Prediction

    Department of Computer Science Stanford University, Flatiron Institute, & SLAC National Lab Stanford, CA 94305, USA · Center for Computational Biology & Center for Computational Mathematics Flatiron Institute New York, NY 10010, USA · Department of Electrical Engineering Stanford University & SLAC National Lab Stanford, CA 94305, USA +2