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Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide...
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LINC02015 modulates the cell proliferation and apoptosis of aortic vascular smooth muscle cells by transcriptional regulation and protein interaction network
Long intergenic nonprotein coding RNA 2015 (LINC02015) is a long non-coding RNA that has been found elevated in various cell proliferation-related...
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Learning the protein language of proteome-wide protein-protein binding sites via explainable ensemble deep learning
Protein-protein interactions (PPIs) govern cellular pathways and processes, by significantly influencing the functional expression of proteins....
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Applications of Circular Dichroism Spectroscopy in Studying Protein Folding, Stability, and Interaction
Circular dichroism (CD) spectroscopy has been extensively used to determine the structure and folding of proteins. It provides valuable information...
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GNNGL-PPI: multi-category prediction of protein-protein interactions using graph neural networks based on global graphs and local subgraphs
Most proteins exert their functions by interacting with other proteins, making the identification of protein-protein interactions (PPI) crucial for...
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A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein–Protein Interaction Networks (PPINs)
Protein–protein interaction plays an important role in the understanding of biological processes in the body. A network of dynamic protein complexes...
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A computational exploration of resilience and evolvability of protein–protein interaction networks
Protein–protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions...
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LASS2 enhances p53 protein stability and nuclear import to suppress liver cancer progression through interaction with MDM2/MDMX
LASS2 functions as a tumor suppressor in hepatocellular carcinoma (HCC), the most common type of primary liver cancer, but the underlying mechanism...
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Systematic comparison of the protein-protein interaction network of bacterial Universal stress protein A (UspA): an insight into its discrete functions
Universal stress protein A (UspA) is ubiquitously over-expressed in varied species of pathogenic bacteria under stress conditions and helps in cell...
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LPI-EnEDT: an ensemble framework with extra tree and decision tree classifiers for imbalanced lncRNA-protein interaction data classification
BackgroundLong noncoding RNAs (lncRNAs) have dense linkages with various biological processes. Identifying interacting lncRNA-protein pairs...
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GCRNN: graph convolutional recurrent neural network for compound–protein interaction prediction
BackgroundCompound–protein interaction prediction is necessary to investigate health regulatory functions and promotes drug discovery. Machine...
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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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Adaptor protein complex interaction map in Arabidopsis identifies P34 as a common stability regulator
Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargoes and coated...
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Rewiring of the protein–protein–metabolite interactome during the diauxic shift in yeast
In budding yeast Saccharomyces cerevisiae , the switch from aerobic fermentation to respiratory growth is separated by a period of growth arrest,...
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Predicting lncRNA–protein interactions through deep learning framework employing multiple features and random forest algorithm
RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and...
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Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network
The arterial aneurysm refers to localized dilation of blood vessel wall and is common in general population. The majority of aneurysm cases remains...
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LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification
BackgroundLong noncoding RNAs (lncRNAs) have dense linkages with a plethora of important cellular activities. lncRNAs exert functions by linking with...
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EnANNDeep: An Ensemble-based lncRNA–protein Interaction Prediction Framework with Adaptive k-Nearest Neighbor Classifier and Deep Models
lncRNA–protein interactions (LPIs) prediction can deepen the understanding of many important biological processes. Artificial intelligence methods...
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Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host–Pathogen Protein–Protein Complexes
Host–pathogen protein–protein interactions are highly complex and dynamic and mediate key steps in pathogen adhesion to host, host invasion, and...
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Navigating the Global Protein–Protein Interaction Landscape Using iRefWeb
iRefWeb is a resource that provides web interface to a large collection of protein–protein interactions aggregated from major primary databases. The...