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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–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 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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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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Building Protein–Protein Interaction Graph Database Using Neo4j
A cell’s various components interact with each other in a coordinated manner to respond to environmental cues and intracellular signals. Compared to...
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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...
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xCAPT5: protein–protein interaction prediction using deep and wide multi-kernel pooling convolutional neural networks with protein language model
BackgroundPredicting protein–protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational...
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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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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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Using PlaPPISite to Predict and Analyze Plant Protein–Protein Interaction Sites
Proteome-wide characterization of protein–protein interactions (PPIs) is crucial to understand the functional roles of protein machinery within cells...
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Centrality Analysis of Protein–Protein Interaction Networks Using R
Proteins are structural and functional components of cells. They interact with each other to drive specific cellular functions. The physical and...
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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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Predicting Protein Interaction Sites Using PITHIA
Several proteins work independently, but the majority work together to maintain the functions of the cell. Thus, it is crucial to know the...
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DL-PPI: a method on prediction of sequenced protein–protein interaction based on deep learning
PurposeSequenced Protein–Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating...
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AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders
BackgroundAptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as...
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Analysis of RNA-Protein Interaction Networks Using RNP-MaP
RNA-protein interactions regulate a myriad of biological functions through formation of ribonucleoprotein complexes. These complexes may consist of...
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Improved compound–protein interaction site and binding affinity prediction using self-supervised protein embeddings
BackgroundCompound–protein interaction site and binding affinity predictions are crucial for drug discovery and drug design. In recent years, many...
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Designing of disruptor molecules to restrain the protein–protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques
Governing protein–protein interaction networks are the cynosure of cell signaling and oncogenic networks. Multifarious processes when aligned with...
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Protein–Protein Interactions in Cancer
Cancerous state is often associated with the aberrant expression of several critical proteins, which in turn, modulate interactions with other...