Optimizing combinatorial structures is core to many real-world problems, such as those encountered in life sciences. For example, one of the crucial steps involved in antibody design is to find an arrangement of amino acids in a protein sequence that improves its binding with a pathogen. Combinatorial optimization of antibodies is difficult due to extremely large search spaces and non-linear objectives. Even for modest antibody design problems, where proteins have a sequence length of eleven, we are faced with searching over 2.05 x 10^14 structures. Applying traditional Reinforcement Learning algorithms such as Q-learning to combinatorial optimization results in poor performance. We propose Structured Q-learning (SQL), an extension of Q-learning that incorporates structural priors for combinatorial optimization. Using a molecular docking simulator, we demonstrate that SQL finds high binding energy sequences and performs favourably against baselines on eight challenging antibody design tasks, including designing antibodies for SARS-COV.
Stable Online and Offline Reinforcement Learning for Antibody CDRH3 Design
University of Freiburg（弗赖堡大学）；Collaborative Research Institute Intelligent Oncology (CRIION)（智能肿瘤学合作研究所（CRIION））；University Medical Center Freiburg（弗赖堡大学医学中心）；BrainLinks-BrainTools（脑连接-脑工具研究中心）
BetterBodies: Reinforcement Learning guided Diffusion for Antibody Sequence Design
University of Freiburg（弗莱堡大学）；Collaborative Research Institute Intelligent Oncology (CRIION)（智能肿瘤学合作研究所（CRIION））；University Medical Center Freiburg（弗莱堡大学医学中心）；BrainLinks-BrainTools
AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusion
Bangladesh University of Engineering and Technology（孟加拉工程与技术大学）；University of California Riverside（加州大学河滨分校）；University of Southern California（南加州大学）；Princeton University（普林斯顿大学）
Generative Co-Design of Antibody Sequences and Structures via Black-Box Guidance in a Shared Latent Space
Center for Frontier AI Research, Agency for Science, Technology and Research, Singapore（前沿人工智能研究中心，科技研究局，新加坡）；Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore（高性能计算研究所，科技研究局，新加坡）；Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore（新加坡食品与生物技术创新研究所，科技研究局，新加坡）
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
Huazhong University of Science and Technology（华中科技大学）；Microsoft Research AI4Science（微软研究院AI4Science）；University of Science and Technology of China（中国科学技术大学）；Peking University（北京大学）
ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning
Georgia State University, Atlanta, USA（佐治亚州立大学）；Georgia Institute of Technology, Atlanta, USA（佐治亚理工学院）；DePauw University, Indiana, USA（德保罗大学）；University of Engineering（工程大学）
Conditional Antibody Design as 3D Equivariant Graph Translation
Tsinghua University（清华大学）；Institute for AI Industry Research (AIR), Tsinghua University（清华大学人工智能产业研究院（AIR））；Beijing Academy of Artificial Intelligence（北京人工智能研究院）；Renmin University of China（中国人民大学）
CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Design
Georgia State University（佐治亚州立大学）；Georgia Institute of Technology（佐治亚理工学院）；University of Engineering and Technology（工程与技术大学）；Lahore University of Management Sciences（拉合尔管理科学大学）
AbAffinity: A Large Language Model for Predicting Antibody Binding Affinity against SARS-CoV-2
Department of Computer Science and Engineering,University of California, Riverside（加州大学河滨分校计算机科学与工程系）；Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont（克劳斯研究生院应用生命科学学院）
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization
School of Artificial Intelligence, University of Chinese Academy of Sciences（中国科学院大学人工智能学院）；Institute of Automation, Chinese Academy of Sciences (CASIA)（中国科学院自动化研究所）；ByteDance Research（字节跳动研究院）；College of Computer Science and Electronic Engineering, Hunan University（湖南大学计算机科学与电子工程学院）
xTrimoABFold: De novo Antibody Structure Prediction without MSA
BioMap Research（BioMap研究院）；Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；Beijing University of Posts and Telecommunications（北京邮电大学）；MBZUAI（穆罕默德·本·扎耶德人工智能大学）
BOAT: Navigating the Sea of In Silico Predictors for Antibody Design via Multi-Objective Bayesian Optimization
MRC Biostatistics Unit, University of Cambridge（剑桥大学生物统计学单位）；Centre for AI, Data Science and Artificial Intelligence, R&D, AstraZeneca（人工智能、数据科学和人工智能研究中心，阿斯利康研发部）
Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding
School of Computer Science, Wuhan University, Wuhan, China（武汉大学计算机学院）；Department of Computing, Macquarie University, Sydney, Australia（麦考瑞大学计算机系）；Wuhan University Shenzhen Research Institute, Shenzhen, China（武汉大学深圳研究院）
A Comprehensive Benchmark of Computational Models for Antibody--Antigen Binding Affinity
McWilliams School of Biomedical Informatics, UTHealth Houston（麦威廉生物医学信息学学院，UT健康科学中心休斯顿分校）；University of Texas Health Science Center（德克萨斯大学健康科学中心）；Korea Advanced Institute of Science and Technology（韩国科学技术院）；Texas Therapeutics Institute（德克萨斯疗法研究所）；Brown Foundation Institute of Molecular Medicine, UTHealth Houston（布朗基金会分子医学研究所，UT健康科学中心休斯顿分校）
AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation
University of Edinburgh（爱丁堡大学）；Technische Universität Darmstadt（达姆施塔特工业大学）；Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；University of Oslo（奥斯陆大学）；American University of Beirut Medical Centre（贝鲁特美国大学医学中心）；University College London（伦敦大学学院）
ABConformer: Physics-inspired Sliding Attention for Antibody-Antigen Interface Prediction
Material Innovation Institute for Life Sciences and Energy（生命科学与能源材料创新研究院）；The University of Hong Kong（香港大学）；Generative AI Research and Development Center（生成式人工智能研究与开发中心）；The Hong Kong University of Science and Technology（香港科学与技术大学）；Computational Immunology Centre（计算免疫学中心）；BayVax Biotech Limited（湾生生物科技有限公司）；School of Biomedical Sciences（生物医学科学学院）
Conditional generation of antibody sequences with classifier-guided germline-absorbing discrete diffusion
Paul G. Allen School of Computer Science and Engineering, University of Washington（华盛顿大学保罗·G·艾伦计算机科学与工程学院）；Life Sciences, Amazon Web Services（亚马逊网络服务生命科学）
S$^2$ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University（浙江大学医学人工智能创新研究院）；College of Pharmaceutical Sciences, Zhejiang University（浙江大学药学院）；School of Medicine, Zhejiang University（浙江大学医学院）；State Key Laboratory of Transvascular Implantation Devices of The Second Affiliated Hospital, Zhejiang University School of Medicine（浙江大学医学院附属第二医院血管植入器件国家重点实验室）；School of Public Health, Zhejiang University（浙江大学公共卫生学院）；Department of Computer Science, UIUC（伊利诺伊大学厄巴纳-香槟分校计算机系）；Zhejiang Key Laboratory of Medical Imaging Artificial Intelligence（浙江省医学影像人工智能重点实验室）
ImmunoAI: Accelerated Antibody Discovery Using Gradient-Boosted Machine Learning with Thermodynamic-Hydrodynamic Descriptors and 3D Geometric Interface Topology
BConformeR: A Conformer Based on Mutual Sampling for Unified Prediction of Continuous and Discontinuous Antibody Binding Sites
Material Innovation Institute for Life Sciences and Energy The University of Hong Kong Hetao SZ-HK Cooperation Zone（生命科学与能源创新材料研究所 香港大学 河套 SZ-HK 合作区）；Hong Kong Generative AI Research and Development Center The Hong Kong University of Science and Technology（香港生成式人工智能研究与发展中心 香港科学大学）；Computational Immunology Centre BayVax Biotech Limited（计算免疫学中心 BayVax 生物技术有限公司）；School of Biomedical Sciences The University of Hong Kong（生物医学科学学院 香港大学）
CAME-AB: Cross-Modality Attention with Mixture-of-Experts for Antibody Binding Site Prediction
Generative AI Research and Development Center The Hong Kong University of Science and Technology（生成式人工智能研究与发展中心 香港科学大学）；MILES The University of Hong Kong（MILES 香港大学）；College of Veterinary Medicine Jilin University（吉林大学兽医学院）；School of Chemistry and Chemical Engineering South China University of Technology（华南理工大学化学与化工学院）；School of Biomedical Sciences The University of Hong Kong（香港大学生物医学科学学院）；Computational Immunology Centre BayVax Biotech Limited（计算免疫学中心 BayVax 生物技术有限公司）；College of Electronic and Information Engineering Southwest University（西南大学电子与信息工程学院）
