Protein Design

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Latest papers 96

23 papers in the last four weeks, up 188% on the four weeks before. 0.1% of all new papers.

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DC-Flow: Target-Conditioned Cyclic Peptide Design via Delayed-Coupling Flow Matching
Oct 11, 2026Yitian Wang, Minjie Cheng, Yaning Cui +3Molecular Generation Generative Modeling
Gaoling School of Artificial Intelligence, Renmin University of China · DP Technology · Cyclon Therapeutics +2
Designing Protein Structures from Natural Language
Oct 9, 2026Joseph Lee, Yanjing Li, Bo Qiang +7Protein Design Generative Modeling
University of Washington · National University of Singapore · Allen Institute for AI (Ai2) +1
DRYLAB-Bench: Benchmarking the Biosecurity Risk of Agentic LLM Mutation Design
Oct 9, 2026Yuzhen Wang, Chunxiao Li, Baichen Le +6LLM Security AI Agent Safety Benchmarks
Shanghai Artificial Intelligence Laboratory · Fudan University
MARCO: The Radioactive Watermark for Protein Generative Models
Oct 6, 2026Huajie Chen, Xin Guo, Yuchen Shi +7Robust Watermarking Diffusion Model Watermarking
Faculty of Data Science, City University of Macau. · CSIRO and Responsible AI Research (RAIR) Centre, Adelaide University.
Bridging the Evidence-to-Execution Gap:A Reflective Agent for Multi-Objective Peptide Design
Oct 5, 2026Haosen Zhang, Yang YangAI Agents for Scientific Discovery Large Language Model-Guided Optimization
School of Agriculture and Biology, Shanghai Jiao Tong University · School of Computer Science, Shanghai Jiao Tong University
Predictor-Guided Latent Space Codon Optimization for Maximizing Protein Expression
Oct 2, 2026Alberto Caron, Tianyu Cui, Dmytro S. Lituiev +13Protein Design Latent Space Optimization
Johnson & Johnson Innovative Medicine · Ellison Institute of Technology Oxford · New Theory AI
Evaluator-in-the-Loop Monte Carlo Tree Search via LLM Agents for Motif Scaffolding in Protein Design
Oct 2, 2026Haotian Hu, Oguzhan Gungordo, Siheng Xiong +1Protein Design Monte Carlo Tree Search
Georgia Institute of Technology
Generative modeling of intrinsically disordered protein regions by reinforcing sparse autoencoder features
Oct 1, 2026Jason X. Liu, Sebastian Ibarraran, Frank Hu +7Autoregressive Language Modeling Sparse Autoencoders
Stanford University
CODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design
Oct 1, 2026Yuanle Mo, Bo Qiang, Haitao Lin +4Molecular Generation Protein Design
Valhalla Technology · The Chinese University of Hong Kong · University of Washington +2
pCoMole: Pareto-Constrained Molecule Editing with Discrete Flows
Oct 1, 2026Tong Chen, Maximilian Holsman, Lin Zhao +1Constrained Generative Modeling Protein Design
Department of Computer and Information Science, University of Pennsylvania · Department of Computer Science, Duke University · Department of Bioengineering, University of Pennsylvania
Structure-aware Reinforcement Learning for Protein Directed Evolution
Sep 30, 2026Zikun Nie, Suyuan Zhao, Yizhen Luo +2Protein Design
Institute of AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · Pharmolix Inc.
Feedback-Calibrated Protein Optimization with Batch-Aligned Tail Arbitration
Sep 29, 2026Zefeng Lin, Xianyong Fang, Tianfan Fu +1Molecular Optimization Protein Design
School of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, China
From Surfaces to Volumes: Registered Geometry for Protein Representation Learning
Sep 28, 2026Siyuan Chen, Cai Zhou, Jinrui Zhang +8Protein-Protein Interaction Prediction 3D Representation Learning
University of British Columbia · Massachusetts Institute of Technology · Carnegie Mellon University +2
Mirror-Score: Calibrated, Inference-only Scoring Exposes the Limits of Sequence-compatibility Ranking in D-peptide Design
Sep 28, 2026Jiada LiProtein-Ligand Binding Affinity Prediction Protein Design
AI Scientist, Albany, NY, USA, 12205
AbGaze: Attentive Geometric Representation Learning for End-to-End Antibody Design
Sep 28, 2026Jiashuo Wang, Siqi Fan, Yizhen Luo +1Geometric Representation Learning Molecular Generation
Institute for AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · PharMolix Inc.
Continuous Variational Synthesis
Sep 28, 2026Alan N. Amin, Mattia G. Gollub, Andrei Slabodkin +2Variational Autoencoders Constrained Generative Modeling
JURA Bio, Inc. Boston, MA 02125, USA
SPINET: Sheaf Protein Inverse Folding Network
Sep 28, 2026Jens Lundsgaard, Colin Mikulski, Zhixuan Yan +1Protein Design
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
Robust Biomolecular Complex Design Across Protein Conformational Landscapes
Sep 27, 2026Qingyuan Zeng, Zongqi Xu, Anglin Liu +7Test-Time Adaptation Multi-Objective Evolutionary Optimization
The Hong Kong University of Science and Technology (Guangzhou) · Southwest Minzu University · Guangzhou University of Chinese Medicine
PhiFold: Towards Dynamic Protein Design with Physics-Structured Covariance Modeling
Sep 26, 2026Yutian Liu, Mujie Lin, LanqianZhang +4Protein Design Physics-Informed Generative Modeling
School of Computer Science, Peking University, Beijing, China · School of Electronic and Computer Engineering, Peking University, Shenzhen, China · School of Life Sciences, Tsinghua University, Beijing 100084, China +2
Spectral Feedback for Test-Time Alignment of Protein Diffusion Models
Sep 24, 2026Shai Dickman, Mert Cemri, Landon Butler +1Diffusion Model Alignment Protein Design
Department of Electrical Engineering and Computer Sciences University of California, Berkeley
PFArena: Benchmarking Language Models for Protein Modification
Sep 24, 2026Yawen Ouyang, Xinbo Zhang, Ziyuan Ma +15Protein Fitness Prediction Protein Language Models
Shanghai Artificial Intelligence Laboratory · Generative Symbolic Intelligence Lab (GenSI), Tsinghua University · Institute for AI Industry Research (AIR), Tsinghua University +1
TorchCraft: Unified binder design by inverting an all-atom structure predictor
Sep 17, 2026TorchCraft Team, Yu Liu, Zhouhanyu Shen +8Molecular Generation Protein Design
Changping Laboratory, Beijing, China
When Edit Flows are Edit Jumps: replicating Edit Flows and EvoFlows
Sep 16, 2026Gabriel Bénédict, Melanie Buechler, Gerard Riera-Solà +3Generative Modeling Protein Design
Visium, Switzerland
Agentic BAIM-LLM Evaluation (ABLE): Benchmarking LLM Use of Protein Design Tools
Sep 5, 2026Bryce Cai, Geetha Jeyapragasan, Samira Nedungadi +2LLM Tool Use LLM Agent Evaluation
SecureBio, Cambridge, MA, USA.
SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign
Sep 3, 2026Jiarui Lu, Yuyang Wang, Yizhe Zhang +4Unified Multimodal Models Generative Modeling
Mila, Université de Montréal, Apple · Apple
Advances in Machine Learning for Directed Evolution: A Five-Year Retrospective
Sep 2, 2026Bruce J. WittmannConstrained Optimization Protein Design
Microsoft, Office of the Chief Scientific Officer
SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding
Sep 1, 2026Handong Wang, Jiaxin Qi, Baisheng Lai +1Protein Language Models Protein Design
Computer Network Information Center, Chinese Academy of Sciences · University of Chinese Academy of Sciences
FAR-DPO: Feasibility-Aware and Robust Direct Preference Optimization for Cyclic Peptide Design
Aug 20, 2026Guofeng Zhang, Rong Han, Xiaoyu Wang +4Molecular Generation Constrained Generative Modeling
Beijing University of Posts and Telecommunications, Beijing, China · Shenzhen University, Shenzhen, China · Tsinghua University, Beijing, China
Off-Manifold Collapse in Guided Protein Language Models
Aug 19, 2026Shuibai Zhang, Xinchi Liu, Fred Zhangzhi Peng +4Protein Language Models Large Language Model-Guided Optimization
University of Wisconsin–Madison · Duke University · Cornell University
Leveraging generative hallucination and biophysics-informed modeling for unified biomolecular sequence-structure co-design
Aug 18, 2026Xuefeng Liu, Mingxuan Cao, Xiao Luo +5Protein Design Molecular Generation
Department of Medicine, University of Florida · Department of Computer Science, University of Chicago · Data Science Institute, University of Chicago +5

Oct 11, 2026J/K move · Enter open · S save

DC-Flow: Target-Conditioned Cyclic Peptide Design via Delayed-Coupling Flow Matching

Yitian Wang, Minjie Cheng, Yaning Cui, Maohua Yang+2

Gaoling School of Artificial Intelligence, Renmin University of China · DP Technology · Cyclon Therapeutics+2

Molecular Generation Generative Modeling Protein Design Protein Binder Design Conditional Flow Matching

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Target-conditioned cyclic peptide design requires coordinating interfacial side chains with macrocyclic closure. Existing end-to-end generators concurrently update geometric and chemical variables from noise, assigning residues to disordered coordinates. Meanwhile, predictor-assisted workflows often get stuck in local traps because they lack feedback in the propose-and-filter stage and ignore 3D structural proposals during sequence search. To overcome the drawbacks of these two paradigms, we propose DC-FLOW, a staged generative framework built around Delayed-Coupling Flow Matching. In principle, DC-FLOW postpones sequence and side-chain activation until a target-conditioned backbone takes shape, resolving structural ambiguity before chemical assignment. Then, it feeds delayed activations back into the backbone, achieving co-evolution of backbone geometry and emerging residue identities by coupling their flows. This mechanism enables more reliable macrocyclic closure and favorable interface packing. For predictor-assisted workflows, DC-FLOW supplies 3D proposals with in-trajectory guidance, enabling cascaded test-time scaling to prune redundant backbones and terminate unpromising refinement early. Extensive experiments show that DC-FLOW improves cyclization fidelity, diversity, and interface energetics, substantially increasing the yield of confident cyclic peptide binders under a fixed final-candidate budget. Our code is available at https://github.com/mianqiu00/DCFlow.