AIMC Topic: Protein Interaction Mapping

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New GO-based measures in multiple network alignment.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: Protein-protein interaction (PPI) networks provide valuable insights into the function of biological systems. Aligning multiple PPI networks may expose relationships beyond those observable by pairwise comparisons. However, assessing the ...
Humans Software Computational Biology Gene Ontology Protein Interaction Mapping Algorithms Protein Interaction Maps
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Towards the prediction of general biomolecular interactions with AI.

Nature methods Aug 1, 2024
Protein Interaction Mapping Algorithms Computational Biology Humans Artificial Intelligence
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Identification of molecular subtypes of dementia by using blood-proteins interaction-aware graph propagational network.

Briefings in bioinformatics Jul 25, 2024
Plasma protein biomarkers have been considered promising tools for diagnosing dementia subtypes due to their low variability, cost-effectiveness, and minimal invasiveness in diagnostic procedures. Machine learning (ML) methods have been applied to en...
Protein Interaction Maps Computational Biology Protein Interaction Mapping Blood Proteins Biomarkers Dementia Machine Learning Algorithms Humans
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INTREPPPID-an orthologue-informed quintuplet network for cross-species prediction of protein-protein interaction.

Briefings in bioinformatics Jul 25, 2024
An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated 'wet lab' experiments. In silico PPI inference methods are ideal tools t...
Algorithms Animals Protein Interaction Maps Neural Networks, Computer Software Species Specificity Protein Interaction Mapping Computational Biology Databases, Protein Humans
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DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning.

Nucleic acids research Jul 5, 2024
Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in predicting t...
Humans Mutation Protein Interaction Maps Point Mutation Protein Interaction Mapping Protein Binding Software Proteins Deep Learning
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MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network.

Bioinformatics (Oxford, England) Jan 5, 2024
MOTIVATION: Protein-protein interaction sites (PPIS) are crucial for deciphering protein action mechanisms and related medical research, which is the key issue in protein action research. Recent studies have shown that graph neural networks have achi...
Neural Networks, Computer Algorithms Computational Biology Proteins Protein Interaction Maps Databases, Protein Protein Interaction Mapping
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Assessment of Protein-Protein Docking Models Using Deep Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2024
Protein-protein interactions are involved in almost all processes in a living cell and determine the biological functions of proteins. To obtain mechanistic understandings of protein-protein interactions, the tertiary structures of protein complexes ...
Protein Conformation Protein Interaction Mapping Proteins Crystallography, X-Ray Software Protein Binding Molecular Docking Simulation Deep Learning Computational Biology
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Machine Learning Methods in Protein-Protein Docking.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2024
An exponential increase in the number of publications that address artificial intelligence (AI) usage in life sciences has been noticed in recent years, while new modeling techniques are constantly being reported. The potential of these methods is va...
Protein Conformation Humans Protein Interaction Mapping Computational Biology Algorithms Proteins Molecular Docking Simulation Machine Learning Protein Binding Software
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Contribution of Artificial Intelligence to the Identification of Protein-Protein Interactions: A Case Study on PAR-3 and Its Partner Adapter Molecule Crk.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2024
Protein-protein interactions (PPIs) are known to be involved in most cellular functions, and a detailed knowledge of such interactions is essential for studying their role in normal and pathological conditions. Significant progress is being made in t...
Protein Binding Computational Biology Proto-Oncogene Proteins c-crk Protein Interaction Mapping Humans Artificial Intelligence Software
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Spatom: a graph neural network for structure-based protein-protein interaction site prediction.

Briefings in bioinformatics Sep 22, 2023
Accurate identification of protein-protein interaction (PPI) sites remains a computational challenge. We propose Spatom, a novel framework for PPI site prediction. This framework first defines a weighted digraph for a protein structure to precisely c...
Neural Networks, Computer Proteins Protein Interaction Mapping Protein Binding
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