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Protein-protein interactions (PPIs) are essentials for many biological processes where two or more proteins physically bind together to achieve their functions. Modeling PPIs is useful for many biomedical applications, such as vaccine…

Biomolecules · Quantitative Biology 2021-12-10 Yang Xue , Zijing Liu , Xiaomin Fang , Fan Wang

Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…

Biomolecules · Quantitative Biology 2024-02-07 Chenqing Hua , Connor Coley , Guy Wolf , Doina Precup , Shuangjia Zheng

The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…

Quantitative Methods · Quantitative Biology 2020-11-30 Jingtao Wang , Xi Li , Hua Zhang

Protein-protein interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has…

Machine Learning · Computer Science 2026-01-13 Fang Wu , Stan Z. Li

Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…

Machine Learning · Computer Science 2022-03-29 Soumyadeep Debnath , Ayatullah Faruk Mollah

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification…

Artificial Intelligence · Computer Science 2026-05-13 Ziqi Gao , Chenyi Zi , Zijing Liu , Ziqiao Meng , Yu Li , Jia Li

Aberrant protein-protein interactions (PPIs) underpin a plethora of human diseases, and disruption of these harmful interactions constitute a compelling treatment avenue. Advances in computational approaches to PPI prediction have closely…

Biomolecules · Quantitative Biology 2025-07-29 François Charih , James R. Green , Kyle K. Biggar

Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…

Biomolecules · Quantitative Biology 2024-07-24 Xiaotong Xu , Alexandre M. J. J. Bonvin

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…

Machine Learning · Computer Science 2025-08-18 Sanket Jantre , Tianle Wang , Gilchan Park , Kriti Chopra , Nicholas Jeon , Xiaoning Qian , Nathan M. Urban , Byung-Jun Yoon

The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and…

Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…

Quantitative Methods · Quantitative Biology 2025-01-30 Jiang Li , Yuan-Ting Li

Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…

Molecular Networks · Quantitative Biology 2023-05-16 Ziyuan Zhao , Peisheng Qian , Xulei Yang , Zeng Zeng , Cuntai Guan , Wai Leong Tam , Xiaoli Li

Protein-protein interaction (PPI) prediction is an instrumental means in elucidating the mechanisms underlying cellular operations, holding significant practical implications for the realms of pharmaceutical development and clinical…

Machine Learning · Computer Science 2025-03-07 Jiang Li , Xiaoping Wang

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…

Quantitative Methods · Quantitative Biology 2017-12-29 Samaneh Aghajanbaglo , Sobhan Moosavi , Maseud Rahgozar , Amir Rahimi

Protein-protein interactions are central mediators in many biological processes. Accurately predicting the effects of mutations on interactions is crucial for guiding the modulation of these interactions, thereby playing a significant role…

Machine Learning · Computer Science 2024-05-29 Yuanle Mo , Xin Hong , Bowen Gao , Yinjun Jia , Yanyan Lan

Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design. The high-throughput experiments…

Molecular Networks · Quantitative Biology 2019-10-11 Andrea Moscatelli

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…

Machine Learning · Computer Science 2024-02-23 Lirong Wu , Yijun Tian , Yufei Huang , Siyuan Li , Haitao Lin , Nitesh V Chawla , Stan Z. Li

In this paper, a new method for PPI (proteinprotein interaction) prediction is proposed. In PPI prediction, a reliable and sufficient number of training samples is not available, but a large number of unlabeled samples is in hand. In the…

Machine Learning · Computer Science 2016-07-19 Amir Ahooye Atashin , Parsa Bagherzadeh , Kamaledin Ghiasi-Shirazi

Drug discovery remains time-consuming, labor-intensive, and expensive, often requiring years and substantial investment per drug candidate. Predicting compound-protein interactions (CPIs) is a critical component in this process, enabling…

Artificial Intelligence · Computer Science 2026-02-06 Zhe Wang , Zijing Liu , Chencheng Xu , Yuan Yao

Biological data are extremely diverse, complex but also quite sparse. The recent developments in deep learning methods are offering new possibilities for the analysis of complex data. However, it is easy to be get a deep learning model that…

Machine Learning · Computer Science 2019-01-21 Florian Richoux , Charlène Servantie , Cynthia Borès , Stéphane Téletchéa
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