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8 papers in the last four weeks, up 167% on the four weeks before. 0.1% of all new papers.

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  1. StabilityArc: Decoding Protein Sequence Embeddings into Generalizable Stability Landscapes

    Sep 30, 2026Aaron L. Feller, Andrew D. Ellington, Claus O. WilkeProteinLattice Mutation

    The University of Texas at Austin Interdisciplinary Life Sciences · The University of Texas at Austin Integrative Biology

  2. Analysis of Quantized and Efficiently Adapted Protein Language Models

    Sep 30, 2026Ilan Yaniv Zeisler, Sebastian Clancy, Pouriya Bayat +8Large Language Model QuantizationLanguage Modeling

    Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada. · Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada. · Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. +2

  3. Structure-aware Reinforcement Learning for Protein Directed Evolution

    Sep 30, 2026Zikun Nie, Suyuan Zhao, Yizhen Luo +2ProteinEvolutionary Optimization Methods

    Institute of AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · Pharmolix Inc.

  4. Does Learning Protein Folding Generalize to Broader Reasoning?

    Sep 30, 2026Yong Liu, Zhanpeng Shi, Yizhou Dang +4Reasoning SkillsProtein

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

  5. Drug-Target Interaction Prediction via Hierarchical Sequential Cross-Attention over Chemical and Protein Language Models

    Sep 28, 2026Khadidja Henni, Hamza Abdelali, Abdelkrim Aries +4ProteinCross-Attention

    I2A institute, T´ELUQ University, Montreal, QC, Canada · LIO, CRCHUM, Montreal, QC, Canada · LCSI, ESI, Algiers, Algeria +3

  6. SPINET: Sheaf Protein Inverse Folding Network

    Sep 28, 2026Jens Lundsgaard, Colin Mikulski, Zhixuan Yan +1Protein Structure PredictionProtein

    Department of Computer Sciences, University of Wisconsin–Madison, Madison, WI, USA · Department of Mathematics, University of Wisconsin–Madison, Madison, WI, USA · Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, WI, USA +4

  7. PFArena: Benchmarking Language Models for Protein Modification

    Sep 24, 2026Yawen Ouyang, Xinbo Zhang, Ziyuan Ma +15ProteinQuality-Driven Selective Mutation

    Shanghai Artificial Intelligence Laboratory · Generative Symbolic Intelligence Lab (GenSI), Tsinghua University · Institute for AI Industry Research (AIR), Tsinghua University +1

  8. MT-ProtBERT: Multi-task Learning ProtBERT for Intrinsically Disordered Proteins Classification with Scarce Data

    Sep 21, 2026Jian Sun, Kingshuk Ghosh, Lilianna Houston +1Protein Structure PredictionProtein

    Department of Computer Science, Ritchie School of Engineering and Computer Science, University of Denver, 2155 E Wesley Ave, Denver, CO 80210 · Department of Surgery, David Geffen School of Medicine at the University of California, Los Angeles, 10833 Le Conte Ave, Los Angeles, CA 90095 · Department of Physics and Astronomy, at the University of Denver, CO 80210 +1

  9. Hyper-Fold: Exploring the Expressive Limit of Sequence-Geometry Learning for Proteins via Hypergraph Modeling

    Aug 29, 2026Yifan Feng, Guanjie Cheng, Shihui Ying +2ProteinGeometric Machine Learning

    1{School of Software, BNRist, THUIBCS}, Tsinghua University, Beijing 100084, China · School of Software Technology, Zhejiang University, Ningbo 315100, China · 3Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai 200072, China +1

  10. DegradeQuery: Counterfactual Tuple Pretraining for Context-Aware PROTAC Degradation Prediction

    Aug 11, 2026Dong Xu, Zhangfan Yang, Jiantao Wu +3ProteinDegradation

    School of Artificial Intelligence, Shenzhen University · EasternDawn · School of Computer Science, University of Nottingham Ningbo

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

    Aug 11, 2026Jiabao Wei, Zilong Geng, Yuze Wang +5ProteinMolecular Dynamics

    1BIT · 3SJTU · 2HUST +2

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

    Jul 30, 2026Shentong Mo, Yatao BianCrystal Structure PredictionProtein

    CMU · NUS

  13. Neural spectroscopy of AlphaFold2 reveals encoded protein conformational landscapes

    Jul 17, 2026Kaustav MehtaConformational EnsemblesProtein

    Independent researcher, India

  14. Two-Stage Fine-Tuning for Protein Sequence Generation with Targeted Amino-Acid Composition

    Jun 26, 2026Violeta Basten-Romero, Rubén Muñoz-Tafalla, Anna María Díaz-Rovira +3Protein DesignProtein Structure Prediction

    Barcelona Supercomputing Center (BSC), Plaça d’Eusebi Güell, 1-3, 08034, Barcelona, Spain · Department of Bioinformatics, School of Mathematics and Statistics (FME), Universitat Politècnica de Catalunya - BarcelonaTech (UPC), 08034 Barcelona, Spain · Nostrum Biodiscovery S.L., Av. Josep Tarradellas, 8-10, 3-2, 08029, Barcelona, Spain +1

  15. PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding

    Jun 25, 2026Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts +3Protein Structure PredictionProtein

    University of California, Irvine · Flagship Pioneering

  16. JEDEL: Zero-Shot DNA-Encoded Library Design for Early-Stage Drug Discovery

    Jun 21, 2026Zygimantas Jocys, Zhanxing Zhu, Henriette M. G. Willems +1Drug DesignDrug Discovery

    School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, United Kingdom. · The ALBORADA Drug Discovery Institute, University of Cambridge,2026 Hills Road, Cambridge, CB2 0AH, United Kingdom.

  17. Enhancing Protein Representation Learning via Manifold Restore Mixing

    Jun 21, 2026Yizhou Dang, Chuang Zhao, Lianbo Ma +3Protein Structure PredictionProtein

    Software College, Northeastern University Shenyang, China · Tianjin University Tianjin, China · School of Computer Science and Engineering, Northeastern University Shenyang, China +1

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

    Jun 20, 2026Rome ThorstensonProteinJacobian

    Independent Researcher

  19. Emyx: Fast and efficient all-atom protein generation

    Jun 12, 2026Nicholas J. Williams, Ward Haddadin, Matteo P. Ferla +6Protein DesignProtein

    Xyme, Oxford, UK

  20. Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs

    Jun 12, 2026Mohamed Mouhajir, Limei Wang, El Houcine Bergou +3Protein Structure PredictionProtein

    College of Computing, UM6P Morocco · Independent USA

  21. Learning Topological Representations of Protein Structure and Dynamics

    Jun 2, 2026Dominik Geng, Florian Graf, Martin Uray +1Molecular DynamicsMolecular Property Prediction

    University of Salzburg, Austria · Josef Ressel Centre for Intelligent and Secure Industrial Automation, University of Applied Sciences, Salzburg, Austria

  22. Structure-Aware Prediction of PROTAC-Mediated Protein Degradability via Graph Neural Networks

    Jun 1, 2026Bryan Cheng, Austin JinProteinStructure-Aware

    Independent Researcher USA

  23. Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent

    Jun 1, 2026Taehan Kim, Sarrah Rose Mikhail Leung, Bharat Mekala +1ProteinMultimodal Search Agents

    UC Berkeley · University of Michigan

  24. Conditioned free-energy density of proteins using unbalanced solutions to constraint satisfaction problems

    May 31, 2026Pratik Worah, Subhash Khot, Srinivasa VaradhanConformational EnsemblesFree Energy Principle

  25. Enhancing Protein-Protein Interaction Prediction with Hierarchical Motif-based Multimodal Protein Embedding

    May 30, 2026Zaifei Yang, Samuel Ping-Man Choi, James KwokProteinUnimodal Encoders

    Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong. · Lee Shau Kee School of Business and Administration, The Hong Kong Metropolitan University, Ho Man Tin, Kowloon, Hong Kong.

  26. ProtStructQA: A Denotation Threshold in Protein Structural Reasoning

    May 30, 2026Aravind Mandiga, Guoming Li, Jin Lu +3Protein Structure PredictionProtein

    University of Georgia

  27. AMix-2: Establishing Protein as a Native Modality in Large Language Models

    May 29, 2026Keyue Qiu, Yixin Wu, Lihao Wang +19ProteinLanguage Modeling

    1Shanghai Artificial Intelligence Laboratory · Institute for AI Industry Research (AIR), Tsinghua University

  28. 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 PredictionProtein

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

  29. SurfDesign: Effective Protein Design on Molecular Surfaces

    May 25, 2026Fang Wu, Shuting Jin, Xiangru Tang +5Protein DesignProtein

    Stanford University Stanford, USA · Wuhan University of Science and Technology Wuhan, China · Yale University New Haven, USA +5

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

    May 21, 2026Taewon Kim, Hyosoon Jang, Hyunjin Seo +6Protein Structure PredictionProtein

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

  31. Protein Fold Classification at Scale: Benchmarking and Pretraining

    May 18, 2026Dexiong Chen, Andrei Manolache, Mathias Niepert +1Protein Structure PredictionProtein

    Max Planck Institute of Biochemistry, Martinsried, Germany · Computer Science Department, University of Stuttgart, Germany · Bitdefender, Romania

  32. Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design

    May 15, 2026Chen Wei, Fanding Xu, Minghao Sun +5Protein DesignProtein

    Xi’an University of Posts & Telecommunications · National University of Singapore · Xi’an Jiaotong University +1

  33. ENSEMBITS: an alphabet of protein conformational ensembles

    May 13, 2026Kaiwen Shi, Carlos OliverConformational EnsemblesProtein

    Department of Computer Science, Vanderbilt University · Center for AI in Protein Dynamics, Vanderbilt University · Department of Molecular Physiology and Biophysics, Vanderbilt University

  34. Decomposing the Generalization Gap in PROTAC Activity Prediction: Variance Attribution and the Inter-Laboratory Ceiling

    May 12, 2026Thor Klamt, Wolfgang Nejdl, Ming TangProteinReceiver Operating Characteristic Area Under The Curve

    L3S Research Center, Leibniz Universität Hannover, Appelstraße 9a, 30167 Hannover, Germany · Institute of Data Science (Knowledge-Based Systems), Faculty of Electrical Engineering and Computer Science,2026 Leibniz Universität Hannover, Appelstraße 9a, 30167 Hannover, Germany

  35. Learning Protein Structure-Function Relationships through Knowledge-guided Representation Decomposition

    May 12, 2026Mingqing Wang, Zhiwei Nie, Athanasios V. Vasilakos +2Protein Structure PredictionProtein

    Shenzhen International Graduate School, Tsinghua University, Shenzhen, China · Pengcheng Laboratory, Shenzhen, China · School of Electronic and Computer Engineering, Peking University, Shenzhen, China +2

  36. Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows

    May 11, 2026Yaochen Rao, Farzaneh Jalalypour, N. M. Anoop Krishnan +1ProteinData-Curation

    Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Gothenburg, SE · Yardi School of Artificial Intelligence, Indian Institute of Technology Delhi, New Delhi, IN

  37. Deep Learning for Protein Complex Prediction and Design

    May 11, 2026Ziwei XieProtein Structure PredictionProtein

    TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO, Chicago, Illinois

  38. SPADE: Faster Drug Discovery by Learning from Sparse Data

    May 6, 2026Rahul Nandakumar, Ben Fauber, Deepayan ChakrabartiDrug DiscoveryProtein

    McCombs School of Business University of Texas at Austin Austin, TX · NVIDIA

  39. PUFFIN: Protein Unit Discovery with Functional Supervision

    Apr 16, 2026Gökçe Uludoğan, Buse Giledereli, Elif Ozkirimli +1ProteinGraph Neural Networks

    Department of Computer Engineering Boğaziçi University Istanbul, Türkiye · Roche Informatics F. Hoffmann-La Roche AG Basel, Switzerland

  40. Sampling at intermediate temperatures is optimal for training large language models in protein structure prediction

    Mar 31, 2026L. Ghiringhelli, A. Zambon, G. TianaProtein Structure PredictionTransformer Architectures

    Department of Physics, via Celoria 16, 20133 Milano, Italy · Department of Physics and INFN, via Celoria 16, 20133 Milano, Italy

  41. Q-BIOLAT: Binary Latent Protein Fitness Landscapes for QUBO-Based Optimization

    Mar 29, 2026Truong-Son HyQuadratic Unconstrained Binary OptimizationProtein

    Department of Computer Science, University of Alabama at Birmingham, Birmingham, Alabama, USA

  42. ProteinZero: Self-Improving Protein Generation via Online Reinforcement Learning

    Jun 9, 2025Ziwen Wang, Jiajun Fan, Ruihan Guo +3Protein DesignProtein

    Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign, Urbana, IL, USA · DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA

  43. ProtScape: A molecular structure and energy-aware representation for protein conformation generation

    Oct 27, 2024Siddharth Viswanath, Xingzhi Sun, Lucas Lee +9Conformational EnsemblesProtein

    Department of Computer Science, Yale University · Department of Genetics, Yale University · Program in Computing, Boise State University +2