Computational and artificial intelligence-based methods for antibody development

Kim, Jisun, McFee, Matthew, Fang, Qiao, Abdin, Osama, Kim, Philip M.·2023·Trends in Pharmacological Sciences
DOI 10.1016/j.tips.2022.12.005

Cited by (178)

Items 101–178 of 178

  1. Computational design of developable therapeutic antibodies: efficient traversal of binder landscapes and rescue of escape mutations
    Frédéric A. Dreyer, Constantin Schneider, Aleksandr Kovaltsuk, Daniel Cutting, Matthew J. Byrne, Daniel Allen Nissley, Newton Wahome, Henry Kenlay, Claire Marks, David Errington et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  2. LlamaAffinity: A Predictive Antibody–Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecture
    Delower Hossain, Ehsan Saghapour, Kevin Song, Jake Y. Chen · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  3. AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies
    Qihong Yan, Xiaohan Huang, Banghui Liu, Yicheng Yao, Huiran Zheng, Yidong Song, Fandi Wu, Zhiyun He, Shaowei Li, Fangli Chen et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
    Marianne Bachmann Salvy, Luca Santuari, Emanuel Schmid‐Siegert, Nikolaos M. R. Lykoskoufis, Ioannis Xénarios, Alaaddin Bulak Arpat · 2024 · mAbs
  5. Multi-criteria decision making and its application to in silico discovery of vaccine candidates for Toxoplasma gondii.
    J. T. Ellis, P. J. Kennedy · 2025 · Vaccine
  6. Artificial Intelligence and Machine Learning Approaches in Designing Immunotherapy in Cancer
    Lokesh Seth, Colton John Ladbury, Arya Amini · 2025 · Cancer treatment and research
  7. Sequence-Based Computational Design of High-Affinity Amphiphilic Copolymers for Protein Targeting: A Machine Learning and Coarse-Grained Simulation Approach
    Shudan Luo, Xu Jia, Xiao Xu · 2025 · Macromolecules
  8. In silico design of stable single-domain antibodies with high affinity
    Zhongyao Zhang, Rob van der Kant, Iva Marković, David Vizarraga, Teresa Garcia, Katerina Maragkou, Javier Delgado Blanco, Damiano Cianferoni, Gabriele Orlando, Gabriel Cia et al. · 2026 · Structure
  9. Nonspecific Cellular Interactions Are a Key Determinant in the Disposition of Fc-Fused Proteins
    Mark A. Bryniarski, Songyu Wang, Aochiu Chen, Brian Coventry, Elif Nihal Korkmaz, Md Tariqul Haque Tuhin, Eunkyung Clare Ko, Devin L. Wakefield, Edward L. LaGory, Hao Wu et al. · 2026 · Molecular Pharmaceutics
  10. Novel loop structure of human IgG1 Fc fused CD38 targeted bispecific antibodies and their anti-tumor effect in acute myeloid leukemia
    Shisen Wang, Manling Chen, Tong Zhou, Chengcai Guo, Zhifeng Yan, Yingxi Xu, Haiyan Xing, Kejing Tang, Zheng Tian, Qing Rao et al. · 2025 · Journal of Translational Medicine
  11. RAIN: a Machine Learning-based identification for HIV-1 bNAbs
    Laurent H. Perez, Mathilde Foglierini · 2024 · Research Square
  12. Enhancing affinity of neutralizing SARS-CoV-2 nanobody through facile structure-guided mutations in CDRs
    Vishakha Singh, Mandar Bhutkar, Shweta Choudhary, Sanketkumar Nehul, Rajesh Kumar, Jitin Singla, Pravindra Kumar, Shailly Tomar · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  13. A Large Language Model Guides the Affinity Maturation of Variant Antibodies Generated by Combinatorial Optimization
    Faisal Bin Ashraf, Zihao Zhang, Karen Paco, Mariana Paco Mendivil, Jordan A. Lay, Animesh Ray, Stefano Lonardi · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  14. AbBFN2: A flexible antibody foundation model based on Bayesian Flow Networks
    Bora Guloglu, Miguel Bragança, Alex Graves, Scott Cameron, Timothy J. Atkinson, Liviu Copoiu, Alexandre Laterre, Thomas D. Barrett · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  15. MultiSAAl: Sequence-informed Antibody-Antigen Interactions Prediction using Multi-scale Deep Learning
    Zexin Lv, Dongliang Hou, Minghua Hou, Suhui Wang, Jian Zhuang, Guijun Zhang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  16. AI Circuit Builder: Bridging Language & Logic
    Saffron Dionysius T, G Rakesh, K Jasmine Mystica · 2025 · International Conference on Visual Analytics and Data Visualization (ICVADV)
  17. Epitope-directed monoclonal antibody production against Staphylococcus aureus enterotoxin B enabled by in silico immunogen design
    Qing Li, Jiafei Mi, Licai Ma, Chenxi Gao, Qiang Ma, Yafang Ding, Liangxi Jia, Hongfang Li, Xuezhi Yu, Kai Wen et al. · 2025 · International Journal of Biological Macromolecules
  18. AI-Driven Protein Discovery: Bridging Computational Innovation and Therapeutic Advancements
    Nur Mohammad Chowdhury, Md Saidul Islam, Subhra Dey, Ranjan Paul, Mohammad Abdul Kadir, Md. Rayhanul Islam, Md Reza Un Nabi, Md Abu Yusuf · 2025 · International Conference on Self Sustainable Artificial Intelligence Systems (ICSSAS)
  19. Immunological Strategies for Enhancing Viral Neutralization and Protection in Antibody-Guided Vaccine Design
    Dimitrina Miteva, Maria Kokudeva, L Tomov, Hristiana Batselova, Tsvetelina Veselinova Velikova · 2025 · Biologics
  20. deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning
    Homa MohammadiPeyhani, Edith Lee, Richard Bonneau, Vladimir Gligorijević, Jae Hyeon Lee · 2025 · Bioinformatics
  21. Advances in Techniques for the Structure and Functional Optimization of Therapeutic Monoclonal Antibodies
    Changxiang He, Weijin Huang, Xi Wu, Huanzhang Xia · 2025 · Biomedicines
  22. Integrative and Emerging Models in Antibody Research: A Comprehensive Review
    Jagadeeswara Reddy Devasani, Girijasankar Guntuku, Prathyusha sarabu, Murali Krishna Kumar Muthyala, Mary Sulakshana Palla, Mallikarjuna Subrahmanyam Volety · 2025 · Antibody Therapeutics
  23. Advancing large-molecule discovery with a unified digital platform for data analysis and workflow management
    Eriberto Noel Natali, Jana Hersch, Christoph Freiberg, Stephan Steigele · 2025 · mAbs
  24. A comprehensive strategy for pandemic preparedness with neutralizing monoclonal antibodies
    Christian Marx, Ralf Piotrowiak, Thomas Schirrmann, Michael Gebinoga, Isabelle Bekeredjian‐Ding, Andreas Schober · 2025 · mAbs
  25. Reprogramming the SARS-CoV-1 Neutralizing Antibody S230 to SARS-CoV-2 via Directed Evolution and Molecular Docking-Based Binding Mode Analysis
    Inji Jung, Dinesh Kumar Sriramulu, Sun‐Gu Lee, Sang Taek Jung · 2025 · ACS Synthetic Biology
  26. Antibody–Drug Conjugates Drug Product Formulation and Process Development, Scalability and Stability Considerations
    Lea L. Sorret, Mamiko Ninomiya, Nils Hillebrandt, David Schmitt, Arundhati Chattopadhyay, Orla McGarvey · 2026 · AAPS PharmSciTech
  27. Artificial intelligence advancements in monoclonal antibody development technology
    Manar Ammar, Mikhail Yu. Samsonov, Evgeniya Gurylina, Daniel R. Bayzigitov · 2026 · Frontiers in Immunology
  28. Recent applications of artificial intelligence in cancer radiotherapy and immunotherapy: current status and future directions
    Qingmiao Shi, Mengjuan Xuan, Chi Lv, Zhibo Zhang, Xiaonan Geng, Di Huang, Xinjun Hu · 2026 · Frontiers in Immunology
  29. Emerging precision medicine in multiple myeloma: clinical and preclinical landscape of T cell, natural killer cell, and macrophages engaging multi-specific antibodies
    Sarra Mestiri, Laila Assami, Zeenath Safira K. M. Yoosuf, Queenie Fernandes, Dina Moustafa Abo El-Ella, Hesham Elsabah, Maysaloun Merhi, Karama Makni‐Maalej, Honar Cherif, Said Dermime et al. · 2026 · Frontiers in Immunology
  30. AI-driven biomolecular design: Modalities, models, and translation
    Mehmoona Azmat, Wenjin Li · 2026 · Biomaterials
  31. Herramientas digitales usadas para la innovación e investigación en la ingeniería: Interpretación individual del fenómeno de la transformación digital del recurso humano
    José Antonio Lara Ramos, Jennyfer Diaz‐Angulo · 2023 · Revista Ing-Nova
  32. Machine-learning-based Structural Analysis of Interactions between Antibodies and Antigens
    Grace Zhang, Xiaohan Kuang, Yuhao Zhang, Yunchao Liu, Zhaoqian Su, Tom Zhang, Yinghao Wu · 2023 · Biosystems
  33. Predicting Antibody–Antigen Interactions with Structure-Aware LLMs: Insights from SARS-CoV-2 Variants
    Faisal Bin Ashraf, Vinz Angelo Madrigal, Stefano Lonardi · 2025 · Journal of Chemical Information and Modeling
  34. Artificial intelligence in antibody design and development: harnessing the power of computational approaches
    Soudabeh Kavousipour, Mahdi Barazesh, Shiva Mohammadi · 2025 · Medical & Biological Engineering & Computing
  35. Computational Analysis of Antibody Binding Mechanisms to the Omicron RBD of SARS-CoV-2 Spike Protein: Identification of Epitopes and Hotspots for Developing Effective Therapeutic Strategies
    Mohammed Alshahrani · 2023 · Chapman University Digital Commons (Chapman University)
  36. Novel antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy
    Hannah Faisal Almubarak, Wuwei Tan, Andrew Daniel Hoffmann, Yuanfei Sun, Juncheng Wei, Lamiaa El-Shennawy, Joshua R Squires, Nurmaa Khund Dashzeveg, Brooke Simonton, Yuzhi Jia et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  37. SARS-CoV-2 Neutralizing Antibodies 2.0
    Youchun Wang · 2024 · Viruses
  38. Can Large Language Models “Read” Biological Sequences? A Systematic Evaluation of In-Context Learning for Antibody Characterization
    Sin-Hang Fung, Zhenghao Zhang, Ran Wang, Chen Miao, Brian Shing‐Hei Wong, Kelly Yichen Li, Chenyang Hong, Jingying Zhou, Kevin Yuk-Lap Yip, Stephen Kwok‐Wing Tsui et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  39. Predicting and Designing Red Fluorescent Protein Variants Using Sequence-to-Function Machine Learning Models
    Ran Ji, Jean Jung, Howard Cheng, Ella Y. Xu, Audrey Wang, Keith Pardee, Yufeng Zhao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Ophiuchus-Ab: A Versatile Generative Foundation Model for Advanced Antibody-Based Immunotherapy
    Yiheng Zhu, Jian Ma, Mingze Yin, Jialu Wu, Lin Tang, Zhiyun Zhang, Qiuyi Li, Shikun Feng, Haiguang Liu, Tao Qin et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  41. Профессиональная компетентность культуролога в контексте прикладной культурологии
    Анастасия Сергеевна Двуреченская · 2013 · Вестник Кемеровского государственного университета культуры и искусств
  42. Understanding the General Principles of T Cell Engagement by Multiscale Computational Simulations
    Zhaoqian Su, Steven C. Almo, Yinghao Wu · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  43. IgG Structure and Function
    Christy A. Thomson · 2024 · Elsevier eBooks
  44. Development and Implementation of Anartificial Intelligence-Based Model for Predicting Drug Sales
    Ying Xiong · 2024 · SSRN Electronic Journal
  45. Novel Bio-Engineering Techniques for Construction of Next-Generation Monoclonal Antibodies in the Framework of Personalized Medicine
    Mahdi Barazesh, Shiva Mohammadi, Sajad Jalili · 2024 · IntechOpen eBooks
  46. Interdisciplinary Approaches to Leverage Biomarker Discovery for Cancer Treatment
    Fatemeh Khatami, Nima Rezaei · 2025 · Interdisciplinary cancer research
  47. Pathological Diagnostics and Microbiology in the Age of Cutting-Edge Technology: Innovations and Future Horizons
    Saja Arkan Jameel Razieg, Haneen Saad Jabbar, MK Hassan, Zainab Haider Jawad kazim, Raham Abdullah Ibrahim Jassim · 2025 · Bright Sky Publications eBooks
  48. Construction of a variable fragment (Fv)-immunoglobulin A (IgA) anti-receptor binding domain (RBD) SARS-CoV-2 library based on IgA from Indonesian COVID-19 survivors
    Adam Darsono, Ernawati Arifin Giri-Rachman, Anita Artarini, David Virya Chen, Tina Lusiany, Dessy Natalia, Patricia Gita Naully, Hendra Saputra Ismanto, Dita Pratama, Ihsanawati Ihsanawati et al. · 2025 · International Journal of Biological Macromolecules
  49. AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees
    Jiaqi Luo, Yiping Zou, Shuai Cheng Li · 2025 · Bioinformatics
  50. Antibody Therapy
    Rachel G. Woodford, Kok Haw Jonathan Lim · 2025 · Elsevier eBooks
  51. MultiSAAl: Sequence-Informed Antibody–Antigen Interaction Prediction Using Multiscale Deep Learning
    Zexin Lv, Dongliang Hou, Minghua Hou, Suhui Wang, Jian Zhuang, Guijun Zhang · 2025 · Journal of Chemical Information and Modeling
  52. Integrative reverse vaccinology approach for identification of a vaccine antigen candidate with immunoprotective and anti-fibrotic potential against Schistosoma japonicum -associated liver fibrosis
    Qin Yang, Jue Wang, Ying Zi Ming, Yu Zhang, Li Ping Wong, Hai Yen Lee · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Integrated antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy
    Hannah Faisal Almubarak, Wuwei Tan, Andrew Daniel Hoffmann, Yuanfei Sun, Juncheng Wei, Lamiaa El-Shennawy, Joshua R Squires, Nurmaa Khund Dashzeveg, Brooke Simonton, Yuzhi Jia et al. · 2025 · iScience
  54. GNNs in drug design
    Yahao Ding, Yiqing Shen, Kai Yi, Yu Guang Wang · 2025 · Elsevier eBooks
  55. DoggifAI: A transformer based approach for antibody caninisation
    Dominik Grabarczyk, Mikołaj Kocikowski, Maciej Parys, Douglas R. Houston, Ted R. Hupp, Javier A. Alfaro, Shay B. Cohen · 2025 · ImmunoInformatics
  56. From Phage Surface to Bedside: Development of Therapeutic Monoclonal Antibodies using Phage Display
    Abhishek Kasana, Khushboo Kapoor, Vaishali Verma · 2025 · Current Pharmacology Reports
  57. Explore antibody repertoire in the era of AI
    Yudi Zhang, Hefei Wang, Chencheng Liu, Fei‐Long Meng · 2025 · Acta Biochimica et Biophysica Sinica
  58. Spin freeze-drying in continuous biomanufacturing: Boon or mirage?
    Teja Kumar Ponduri, G.S.N. Koteswara Rao · 2025 · Journal of Drug Delivery Science and Technology
  59. Targeting mycobacterial PPE65 protein to develop a multi-epitope vaccine candidate against tuberculosis
    Monalisa Swargiary, Rahila Qureshi, Jyotisha, Insaf Ahmed Qureshi · 2026 · International Journal of Biological Macromolecules
  60. AI and IoT Integration in Biomolecular Sensing Systems
    J. M. Radhika, J. Ajayan, Sandip Bhattacharya, S. Sreejith · 2025 · Nanostructure science and technology
  61. High-affinity optimization potential of the virus neutralizing antibody with twin cysteine-stabilized complementarity-determining region 3
    Jing Li, Dan-Dan Zeng, Qi Yin, Sen Zhang, Dongsheng Zhao, Yue Zhang, Zhang Zhang, Fan Tong, Zhongpeng Zhao, Tao Jiang et al. · 2026 · Frontiers in Cellular and Infection Microbiology
  62. Journey of therapeutic antibodies: from discovery to future
    Abhay H. Pande, Sandeep, J. Anakha · 2026 · Exploration of Drug Science
  63. Deciphering Molecular Charge Anisotropy: The Case of Antibody Solutions
    Fabrizio Camerin, Susana Marín-Aguilar, Anna Stradner, Peter Schurtenberger, Emanuela Zaccarelli · 2026 · Small
  64. Trop2 immunoPET/CT in clinical practice: facts and challenges
    Ailin Deng, Wenzhi Jia, Gang Huang, Jianjun Liu, Weijun Wei · 2026 · Drug Discovery Today
  65. Engineering nasally delivered IgM antibodies for respiratory viral infections
    Ashwin Kumar Ramesh, Zhiqiang An · 2026 · hLife
  66. Robust Conditional Diffusion with Noisy Templates for Antibody Sequence–Structure Design
    Pi Liu, Chenyang Yan, Chenyang Yan, Xiao Liu, Shujian Huang, 吴镇, Jianbing Zhang · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  67. AI-Driven Design Platforms of Next-Generation Antibody Therapeutics
    Yue Wang, Afsheen Saba, Yue Ran, Kiran Shehzadi, Q Zhang, Liang Jianhua, Mingjia Yu · 2026 · Topics in Current Chemistry
  68. 243Chapter 13 Emerging Technologies at the Intersection of AI and Biotechnology
    Shallu Saini, Manuj Saini, Hardeep Singh Tuli, Priti Duhan · 2026 · De Gruyter eBooks
  69. Machine Learning Models for Local Optimization of Red Fluorescent Protein Variants in a Low-Data Setting
    Ran Ji, Jean Jung, Howard Cheng, Ella Xu, Audrey Wang, Victor Mun-Sing Sit, Keith Pardee, Yufeng Zhao · 2026 · Journal of Chemical Information and Modeling
  70. Antigen–antibody interactions in precision medicine: Molecular mechanisms, targeted drug delivery, and nanomedicine applications
    Zahra Izadiyan, Roshafima Rasit Ali, Thomas J. Webster, Zahra Maghareh Esfahan, Kamyar Shameli · 2026 · Letters in Drug Design & Discovery
  71. A USP15/KRT17-associated 13-gene prognostic cluster and functional validation in EGFR-mutant lung adenocarcinoma
    Jiamin Huang, Yi Huang, Qi Yuan, Aiwei Tang, Minzhe Su, Yuanyuan Li, Zhen Gan, Xiuxiu Yang, Junyi Song, Yaokai Ye et al. · 2026 · Respiratory Research
  72. PAC-Net: A physics-guided multimodal hybrid network for antibody-antigen interaction prediction
    Songjian Wei, ChunYan Tang, Yan Chen, Jinxiong Zhang, Jiayang Tan, Lilan Lv · 2026 · Journal of Biomedical Informatics
  73. Protein modification: convergence of artificial intelligence, synthetic biology, and nano-assembly
    Peng Liu, Di Wu, Zhong Zhang, Wen Li, Wanchao Chen, Yaxing Zhao, Yan Yang · 2026 · Food Chemistry
  74. A p53R273H-selective bispecific T cell engager: Computational design and functional validation
    Nhan Huynh, Thu-My Thi Nguyen, Ngoc Thi Bui, Thao-Nguyen Ho Nguyen, Diem TP Tran, Hoai-Nghia Nguyen, Cuong Thach Nguyen · 2026 · Molecular Therapy Oncology
  75. Emerging advances in multimodal AI in cancer immunotherapy: from multi-scale data integration to clinical decision support
    Wenjie Zhang, Zeyu Luo, Kaijie Liu, Yuzhu Wang, Yongying Hou, Xiaotan Su, Xisong Wu, Cheng Miao, Qin Liu, Zongsheng He et al. · 2026 · 中国科学通报：英文版
  76. Engineered antibodies: the molecular workhorses of the immune system as therapeutics
    Aditi Singh, Sucharita Shadangi, Souptik Bag, Soumendra Rana · 2026 · Elsevier eBooks
  77. Utilizing Language Models to Forecast Antibody Activity against Influenza A
    Giuseppe Sautto · 2026 · ImmPort
  78. SprintX: mitigating data scarcity in antibody design via synthetic structural prior knowledge dataset
    Ryong Heo, Dahyeon Lee, Jaeho Jung, Byung Ju Kim, Chihyun Park · 2026 · mAbs