AIMC Topic: Protein Interaction Mapping

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MVGNN-PPIS: A novel multi-view graph neural network for protein-protein interaction sites prediction based on Alphafold3-predicted structures and transfer learning.

International journal of biological macromolecules Jan 21, 2025
Protein-protein interactions (PPI) are crucial for understanding numerous biological processes and pathogenic mechanisms. Identifying interaction sites is essential for biomedical research and targeted drug development. Compared to experimental metho...
Binding Sites Protein Interaction Mapping Graph Neural Networks Proteins Models, Molecular Protein Conformation Protein Binding Computational Biology Neural Networks, Computer Algorithms
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PPILS: Protein-protein interaction prediction with language of biological coding.

Computers in biology and medicine Jan 19, 2025
Protein-protein interactions within a cell are essential for various fundamental biological processes. Computational techniques have arisen in bioinformatics due to the challenging and resource-intensive nature of experimental protein pair interactio...
Proteins Databases, Protein Protein Interaction Mapping Protein Interaction Maps Computational Biology Humans Machine Learning
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Supervised learning approaches for predicting Ebola-Human Protein-Protein interactions.

Gene Jan 17, 2025
The goal of this research work is to predict protein-protein interactions (PPIs) between the Ebola virus and the host who is at risk of infection. Since there are very limited databases available on the Ebola virus; we have prepared a comprehensive d...
Computational Biology Support Vector Machine Databases, Protein Humans Protein Interaction Maps Protein Interaction Mapping Hemorrhagic Fever, Ebola Ebolavirus Gene Ontology Supervised Machine Learning Viral Proteins Host-Pathogen Interactions
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Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning.

Biomolecules Jan 17, 2025
Protein-Protein Interaction (PPI) prediction plays a pivotal role in understanding cellular processes and uncovering molecular mechanisms underlying health and disease. Structure-based PPI prediction has emerged as a robust alternative to sequence-ba...
Proteins Protein Conformation Machine Learning Proteomics Humans Deep Learning Computational Biology Protein Interaction Mapping
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MAGPIE: A Machine Learning Approach to Decipher Protein-Protein Interactions in Human Plasma.

Journal of proteome research Jan 7, 2025
Immunoprecipitation coupled to tandem mass spectrometry (IP-MS/MS) methods are often used to identify protein-protein interactions (PPIs). While these approaches are prone to false positive identifications through contamination and antibody nonspecif...
Blood Proteins Tandem Mass Spectrometry Immunoprecipitation Protein Interaction Maps Proteomics Protein Interaction Mapping Machine Learning Humans Algorithms
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Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein-Protein Interactions.

Journal of chemical information and modeling Jan 7, 2025
Predicting protein-protein interaction (PPI) binding affinities in unseen protein complex clusters is essential for elucidating complex protein interactions and for the targeted screening of peptide- or protein-based drugs. We introduce MCGLPPI++, a ...
Protein Binding Machine Learning Proteins Receptors, Antigen, T-Cell Protein Interaction Mapping
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Deep representation learning of protein-protein interaction networks for enhanced pattern discovery.

Science advances Dec 18, 2024
Protein-protein interaction (PPI) networks, where nodes represent proteins and edges depict myriad interactions among them, are fundamental to understanding the dynamics within biological systems. Despite their pivotal role in modern biology, reliabl...
Humans Algorithms Protein Interaction Maps Computational Biology Deep Learning Protein Interaction Mapping
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Novel artificial intelligence-based identification of drug-gene-disease interaction using protein-protein interaction.

BMC bioinformatics Dec 18, 2024
The evaluation of drug-gene-disease interactions is key for the identification of drugs effective against disease. However, at present, drugs that are effective against genes that are critical for disease are difficult to identify. Following a diseas...
Computational Biology Drug Repositioning Protein Interaction Mapping Neoplasms Antineoplastic Agents Humans Artificial Intelligence
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Integration of biological data via NMF for identification of human disease-associated gene modules through multi-label classification.

PloS one Dec 12, 2024
Proteins associated with multiple diseases often interact, forming disease modules that are critical for understanding disease mechanisms. This study integrates protein-protein interactions (PPIs) and Gene Ontology data using non-negative matrix fact...
Computational Biology Disease Protein Interaction Maps Protein Interaction Mapping Gene Ontology Humans Gene Regulatory Networks Genetic Predisposition to Disease Algorithms
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An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Protein-protein interactions (PPIs) are essential to understanding cellular mechanisms, signaling networks, disease processes, and drug development, as they represent the physical contacts and functional associations between proteins. Recent advances...
Protein Interaction Maps Humans Computational Biology Graph Neural Networks Databases, Protein Neural Networks, Computer Proteins Protein Interaction Mapping Algorithms
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