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Title
Japanese: 
English:SpatialPPI:three-dimensional space protein-protein interaction prediction with AlphaFold Multimer 
Author
Japanese: 胡 文星, 大上雅史.  
English: Wexing Hu, Masahito Ohue.  
Language English 
Journal/Book name
Japanese: 
English:Computational and Structural Biotechnology Journal 
Volume, Number, Page Volume 23        page 1214-1225
Published date Dec. 2024 
Publisher
Japanese:エルゼビア 
English:ELSEVIER 
Conference name
Japanese: 
English: 
Conference site
Japanese: 
English: 
Official URL https://www.sciencedirect.com/science/article/pii/S200103702400062X?via%3Dihub
 
DOI https://doi.org/10.1016/j.csbj.2024.03.009
Abstract Rapid advancements in protein sequencing technology have resulted in gaps between proteins with identified sequences and those with mapped structures. Although sequence-based predictions offer insights, they can be incomplete due to the absence of structural details. Conversely, structure-based methods face challenges with respect to newly sequenced proteins. The AlphaFold Multimer has remarkable accuracy in predicting the structure of protein complexes. However, it cannot distinguish whether the input protein sequences can interact. Nonetheless, by analyzing the information in the models predicted by the AlphaFold Multimer, we propose a highly accurate method for predicting protein interactions. This study focuses on the use of deep neural networks, specifically to analyze protein complex structures predicted by the AlphaFold Multimer. By transforming atomic coordinates and utilizing sophisticated image-processing techniques, vital 3D structural details were extracted from protein complexes. Recognizing the significance of evaluating residue distances in protein interactions, this study leveraged image recognition approaches by integrating Densely Connected Convolutional Networks (DenseNet) and Deep Residual Network (ResNet) within 3D convolutional networks for protein 3D structure analysis. When benchmarked against leading protein-protein interaction prediction methods, such as SpeedPPI, D-script, DeepTrio, and PEPPI, our proposed method, named SpatialPPI, exhibited notable efficacy, emphasizing the promising role of 3D spatial processing in advancing the realm of structural biology.

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