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Protein–Protein Interaction Network Exploration Using Cytoscape
As the protein–protein interaction (PPI) data increase exponentially, the development and usage of computational methods to analyze these datasets...
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Protein–Protein Interaction Network Analysis Using NetworkX
In recent years, extracting information from biological data has become a particularly valuable way of gaining knowledge. Molecular interaction...
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Protein features fusion using attributed network embedding for predicting protein-protein interaction
BackgroundProtein-protein interactions (PPIs) hold significant importance in biology, with precise PPI prediction as a pivotal factor in...
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Identification of the bacteriophage nucleus protein interaction network
In the arms race between bacteria and bacteriophages (phages), some large-genome jumbo phages have evolved a protein shell that encloses their...
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Computational prediction of protein–protein interactions’ network in Arabidopsis thaliana
The study of protein–protein interactions (PPIs) has been a major factor in understanding the function of proteins. The development of diverse...
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Small protein complex prediction algorithm based on protein–protein interaction network segmentation
BackgroundIdentifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein...
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Multi-view heterogeneous molecular network representation learning for protein–protein interaction prediction
BackgroundProtein–protein interaction (PPI) plays an important role in regulating cells and signals. Despite the ongoing efforts of the bioassay...
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Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions
BackgroundDevelopment of new methods for analysis of protein–protein interactions (PPIs) at molecular and nanometer scales gives insights into...
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Predicting Drug-Target Affinity Using Protein Pocket and Graph Convolution Network
Drug–target affinity (DTA) plays a crucial role in the discovery and development of pharmaceuticals. The localized structure of protein pockets plays...
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SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures
BackgroundThe relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a...
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A protein network refinement method based on module discovery and biological information
BackgroundThe identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover...
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Golgi-associated retrograde protein (GARP) complex-dependent endosomes to trans Golgi network retrograde trafficking is controlled by Rab4b
BackgroundThe trafficking of cargoes from endosomes to the trans -Golgi network requires numerous sequential and coordinated steps. Cargoes are...
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Quantification of Protein Exit at the Trans-Golgi Network
With one-third of all newly synthesized proteins entering the secretory pathway, correct protein sorting is essential for cellular homeostasis. In...
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SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction
BackgroundProtein-protein interactions (PPIs) dominate intracellular molecules to perform a series of tasks such as transcriptional regulation,...
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Efficient link prediction in the protein–protein interaction network using topological information in a generative adversarial network machine learning model
BackgroundThe investigation of possible interactions between two proteins in intracellular signaling is an expensive and laborious procedure in the...
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The Protein Network Essential for Ribosome Biogenesis Organized by the Multifunctional Rrp5 Protein (A Review)
AbstractThe production of ribosomes occurs through a complex pathway that requires the precise cleavage of pre-rRNA to generate four mature precursor...
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Towards a structurally resolved human protein interaction network
Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to...
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Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network
As one of the most important post-translational modifications (PTMs), protein phosphorylation plays a key role in a variety of biological processes....
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Prioritization of Trypanosoma brucei editosome protein interactions interfaces at residue resolution through proteome-scale network analysis
BackgroundTrypanosoma brucei is the causative agent for trypanosomiasis in humans and livestock, which presents a growing challenge due to drug...
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Protein–Protein Interactions: Co-immunoprecipitation
Proteins often do not function as single substances but rather as team players in a dynamic network. Growing evidences show that protein–protein...