Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

Cited by (141)

Items 101–141 of 141

1. Predicting Antibody Affinity Changes upon Mutation Based on Unbound Protein Structures
   Zhengshan Chen, Song He, Xiangyang Chi, Xiaochen Bo · 2025 · International Journal of Molecular Sciences
2. 3D ‐ ΔΔG : A Dual‐Channel Prediction Model for Protein–Protein Binding Affinity Changes Following Mutation Based on Protein 3D Structures
   Yuxiang Wang, Yibo Zhu, Xiumin Shi, Lu Wang · 2025 · Proteins Structure Function and Bioinformatics
3. Recent advances in antibody optimization based on deep learning methods
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4. AFToolkit: a framework for molecular modeling of proteins with AlphaFold-derived representations
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5. Predicting the Effects of Charge Mutations on the Second Osmotic Virial Coefficient for Therapeutic Antibodies via Coarse-Grained Molecular Simulations and Deep Learning Methods
   Hassan Shahfar, Christopher J. Roberts · 2025 · Molecular Pharmaceutics
6. Deep learning for affinity prediction and interface prediction in molecular interactions
   Yatao Bian, Huaijin Wu, Junchi Yan · 2025 · Elsevier eBooks
7. AFP-specific T cell receptors with fine-tuning affinity induce durable tumor remission in mice and acquire pan-HLA-A∗02 recognition
   Cheng Huang, Jiajia Du, Jun Li, Ya-Hao Guo, Qingjia Yan, Sha Wu, Xihe Chen, Tein Foong Leong, Siyun Chen, An‐Da Zheng et al. · 2026 · Molecular Therapy
8. Artificial intelligence advancements in monoclonal antibody development technology
   Manar Ammar, Mikhail Yu. Samsonov, Evgeniya Gurylina, Daniel R. Bayzigitov · 2026 · Frontiers in Immunology
9. GCAT: A network model of mutational influences between amino acid positions in PSD95pdz3
   Lorenza Pacini, Claire Lesieur · 2022 · Frontiers in Molecular Biosciences
10. Understanding the contagiousness of Covid-19 strains: A geometric approach
    Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jack A. Tuszyński, Federica Marcolin · 2023 · Journal of Molecular Graphics and Modelling
11. A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment
    Yitong Lv, Gong He, Xuechao Liu, Hao Jia, Lei Xu, Zhiwei Sun, Changyuan Yu, Lida Xu · 2024 · PLoS Computational Biology
12. Deep learning for discriminating non-trivial conformational changes in molecular dynamics simulations of SARS-CoV-2 spike-ACE2
    Lucas Moraes dos Santos, José Gutembergue de Mendonça, Yan Jeronimo Gomes Lobo, Leonardo Henrique França de Lima, Gerd Bruno Rocha, Raquel C. de Melo-Minardi · 2024 · Scientific Reports
13. Physical-Chemical Features Selection Reveals That Differences in Dipeptide Compositions Correlate Most with Protein-Protein Interactions
    Hamid Teimouri, Angela Medvedeva, Anatoly B. Kolomeisky · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
14. abCAN: a Practical and Novel Attention Network for Predicting Mutant Antibody Affinity
    Chen Gong, Yunyao Shen, Hongjia Liu, Wenlong Ming · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
15. Sequence-aware Prediction of Point Mutation-induced Effects on Protein-Protein Binding Affinity using Deep Learning
    Jian Zhuang, Zonghui Li, Suhui Wang, Ren‐Chao Zheng, Guijun Zhang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
16. Geometric and topological AI for molecular sciences
    JunJie Wee · 2023 · DR-NTU (Nanyang Technological University)
17. An introduction to the application of deep learning in the biomedical field
    Ruisong WANG, Shengnan WANG, Tieliu SHI · 2024 · Scientia Sinica Vitae
18. Exploring Protein-DNA Binding Residue Prediction and Consistent Interpretability Analysis Using Deep Learning
    Yufan Liu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
19. An Antigen Design Method Based on Molecular Dynamics and Deep Learning
    Hongtu Li, Shuangyan Zhou · 2024 · IEEE International Conference on Medical Artificial Intelligence (MedAI)
20. Molecular structure and role of microbial proteins: a delimitation employing bioinformatics techniques
    Debanjan Saha, Nayan Jyoti Borah, Afrin Mamud · 2025 · Elsevier eBooks
21. PackPPI : An integrated framework for protein–protein complex side‐chain packing and ΔΔG prediction based on diffusion model
    Jingkai Zhang, Yuanyan Xiong · 2025 · Protein Science
22. Trends Assessment of the Genetic Mutation Induced Protein-Protein Interaction Variation via Protein Large Language Driven Method
    Zhe-Jun Kuang, Yun-Kai Li, Zhe Liu, Jian Zhao, Li-Juan Shi, Akira-Kawai, Han Wang · 2025 · bioRxiv
23. A systematic review of spatial epidemiological modeling approaches applied during the COVID-19 pandemic
    Kayode Oshinubi, Ye Chen, Eck Doerry, Esma S. Gel, Crystal M. Hepp, Timothy Lant, Sanjay Mehrotra, Samantha J. Sabo, Joseph R. Mihaljevic · 2026 · BMC Public Health
24. GNNs in drug design
    Yahao Ding, Yiqing Shen, Kai Yi, Yu Guang Wang · 2025 · Elsevier eBooks
25. USP-ddG: a unified structural paradigm with data efficacy and mixture-of-experts for predicting mutational effects on protein–protein interactions
    Guanglei Yu, Xuehua Bi, Qichang Zhao, Jianxin Wang · 2026 · Bioinformatics
26. Additional file 1 of Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method
    Li, Shan Shan, Zhao Ming Liu, Jiao Li, Yi Bo Ma, Ze Yuan Dong, Jun Wei Hou, Fu Jie Shen, Wei Bu Wang, Li, Qi Ming, Ji Guo Su · 2024 · Figshare
27. Additional file 2 of Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method
    Li, Shan Shan, Zhao Ming Liu, Jiao Li, Yi Bo Ma, Ze Yuan Dong, Jun Wei Hou, Fu Jie Shen, Wei Bu Wang, Li, Qi Ming, Ji Guo Su · 2024 · Figshare
28. SE3Bind: SE(3)-equivariant model for antibody-antigen binding affinity prediction
    Anushriya Subedy, Siddharth Bhadra-Lobo, Guillaume Lamoureux · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
29. VQH-AM: Vector Quantization-Augmented Heterogeneous Graph Learning for Antibody Affinity Maturation Prediction
    甄卓文, Tengfei Ma, Jiaxuan Li, Dashun Zheng, Patrick Cheong‐Iao Pang, Yiping Liu, Xiangxiang Zeng · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
30. Multi-Scale Feature Fusion Network for the Prediction of Protein-Protein Binding Affinity Changes upon Mutations
    Hao Zhang, Yang Liu, Lei Yu, Zejie Wang, Yifei Liu, Maozu Guo · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
31. CrossAffinity: A Sequence-Based Protein-Protein Binding Affinity Prediction Tool Using Cross-Attention Mechanism
    Jia Sheng Guan, Zechen Wang, Yuguang Mu · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
32. MutPPI+: a multimodal framework for predicting mutation effects on protein–protein interactions via mutation-path-based data augmentation
    Juntao Deng, Miao Gu, Pengyan Zhang, Tao Liu, Guansong Hu, Mingyu Dong, Yabin Zhang, Yizhen Song, Yunfan Zhang, Min Liu et al. · 2026 · Briefings in Bioinformatics
33. Ultra-sensitive detection of receptor binding domain of SARS-CoV-2 based on artificial intelligence assisted antibody selection and antibody‒nucleic acid conjugation signal amplification
    Jiatong Liu, Wenfan Chen, Xiufeng Li, Yuanyuan Luo, Qiaomin Li, Wenbin Zhao, Qiaojun He, Su Zeng, Zhan Mei Zhou, Sheng Cai · 2026 · Acta Pharmaceutica Sinica B
34. Enhancing mutation impact prediction in protein-protein interactions through interpretable graph-based multi-level feature interactions
    Shiwei Wu, Nan Xu, Xiaohui Xin, Min Zhang, Haoliang Liu, Hongjia Zhu, Zhenyu Wei, Chengkui Zhao, Li Yu, Weixing Feng · 2026 · Bioinformatics
35. Towards Expressive Graph Neural Networks : Theory, Algorithms, and Applications
    Georgios Dasoulas · 2022
36. New computational approaches to study the effect of genetic mutations on the topology of protein-protein interaction networks
    Yasser Mohseni Behbahani · 2022 · theses.fr (ABES)
37. Robust and interpretable machine learning for affinity prioritization of designed protein interactors
    Yu‐Chen Lo, Keng‐Fu Chang, I-Hsuan Chu, Lu-Yi Chen, Kuen‐Phon Wu · 2026 · Protein Science
38. Cross-Subject Event-Related Potential Classification via Multi-View Based Contrastive Learning
    Chaochen Chen, Lugui Xia, Jie Zhuang, Qian Qian, Hongfei Ji, Jie Li · 2026 · Brain Connectivity
39. Predicting Antibody–Antigen Mutation ΔΔ G via Side-Specific Protein Language Models and Paired Geometric Graph Learning
    Wenchi Ge, Qijia Yu, Jincen Shuai, Qi Zhao · 2026 · Journal of Chemical Information and Modeling
40. Codon Mutation Probability Modeling in SARS-CoV-2
    Shivam Kumar Thakur, A Apzana Nizam, Noel Jeygar Robert V · 2026 · IEEE Access
41. An inverse-protein-folding pre-trained model for predicting the mutational effects in protein-protein interactions
    Sihong Mao, Siwei Meng, Ye Xiang · 2026 · iScience