AIMC Topic: Protein Interaction Mapping

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A multi-objective evolutionary algorithm for detecting protein complexes in PPI networks using gene ontology.

Scientific reports May 15, 2025
Detecting protein complexes is crucial in computational biology for understanding cellular mechanisms and facilitating drug discovery. Evolutionary algorithms (EAs) have proven effective in uncovering protein complexes within networks of protein-prot...
Gene Ontology Protein Interaction Mapping Algorithms Protein Interaction Maps Computational Biology Saccharomyces cerevisiae
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Negative sampling strategies impact the prediction of scale-free biomolecular network interactions with machine learning.

BMC biology May 9, 2025
BACKGROUND: Understanding protein-molecular interaction is crucial for unraveling the mechanisms underlying diverse biological processes. Machine learning (ML) techniques have been extensively employed in predicting these interactions and have garner...
Computational Biology Machine Learning Protein Interaction Mapping Protein Interaction Maps
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Molecular Association Assay Systems for Imaging Protein-Protein Interactions in Mammalian Cells.

Biosensors May 8, 2025
Molecular imaging probes play a pivotal role in assaying molecular events in various physiological systems. In this study, we demonstrate a new genre of bioluminescent probes for imaging protein-protein interactions (PPIs) in mammalian cells, named t...
Artificial Intelligence Animals Humans Luminescent Measurements Molecular Imaging Protein Interaction Mapping Protein Binding Mice
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Topology-driven negative sampling enhances generalizability in protein-protein interaction prediction.

Bioinformatics (Oxford, England) May 6, 2025
MOTIVATION: Unraveling the human interactome to uncover disease-specific patterns and discover drug targets hinges on accurate protein-protein interaction (PPI) predictions. However, challenges persist in machine learning (ML) models due to a scarcit...
Protein Interaction Mapping Protein Binding Computational Biology Humans Databases, Protein Machine Learning Binding Sites Proteins
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The influence of prompt engineering on large language models for protein-protein interaction identification in biomedical literature.

Scientific reports May 3, 2025
Identifying protein-protein interactions (PPIs) is a foundational task in biomedical natural language processing. While specialized models have been developed, the potential of general-domain large language models (LLMs) in PPI extraction, particular...
Protein Interaction Mapping Large Language Models Humans Natural Language Processing Computational Biology Data Mining
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Gated-GPS: enhancing protein-protein interaction site prediction with scalable learning and imbalance-aware optimization.

Briefings in bioinformatics May 1, 2025
In protein-protein interaction site (PPIS) prediction, existing machine learning models struggle with small datasets, limiting their predictive accuracy for unseen proteins. Additionally, class imbalance in protein complexes, where binding residues c...
Humans Machine Learning Computational Biology Proteins Databases, Protein Algorithms Protein Binding Binding Sites Protein Interaction Mapping
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GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes.

Bioinformatics (Oxford, England) Mar 29, 2025
MOTIVATION: Leveraging deep learning for the representation learning of Gene Ontology (GO) and Gene Ontology Annotation (GOA) holds significant promise for enhancing downstream biological tasks such as protein-protein interaction prediction. Prior ap...
Molecular Sequence Annotation Gene Ontology Deep Learning Protein Interaction Mapping Software Computational Biology Algorithms
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Unlocking protein networks with Predictomes: The SPOC advantage.

Molecular cell Mar 20, 2025
In this issue of Molecular Cell, Schmid and Walter present "Predictomes," a machine-learning-based platform that utilizes AlphaFold-Multimer (AF-M) to identify high-confidence protein-protein interactions (PPIs). Their SPOC classifier is better than ...
Proteins Protein Interaction Mapping Protein Interaction Maps Computational Biology Humans Machine Learning
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Improved in Silico Identification of Protein-Protein Interactions Using Deep Learning Approach.

IET systems biology Jan 1, 2025
Protein-protein interactions (PPIs) perform significant functions in many biological activities likewise gene regulation, metabolic pathways and signal transduction. The deregulation of PPIs may cause deadly diseases, such as cancer, autoimmune, pern...
Computer Simulation Animals Computational Biology Protein Interaction Mapping Deep Learning Humans
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EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces.

Bioinformatics (Oxford, England) Nov 1, 2024
MOTIVATION: Protein-protein interactions are essential for a variety of biological phenomena including mediating biochemical reactions, cell signaling, and the immune response. Proteins seek to form interfaces which reduce overall system energy. Alth...
Neural Networks, Computer Protein Interaction Mapping Software Proteins Protein Conformation Algorithms Deep Learning Protein Binding Molecular Docking Simulation Computational Biology
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