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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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Network pharmacology, molecular docking, and molecular dynamics simulation analysis reveal the molecular mechanism of halociline against gastric cancer
Halociline, a derivative of alkaloids, was isolated from the marine fungus Penicillium griseofulvum by our group. This remarkable compound exhibits...
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Molecular Mechanism of Yangshen Maidong Decoction in the Treatment of Chronic Heart Failure based on Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulations
Chronic heart failure (CHF) is a complex multifactorial clinical syndrome leading to abnormal cardiac structure and function. The severe form of this...
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Exploring the molecular mechanism of Epimedium for the treatment of ankylosing spondylitis based on network pharmacology, molecular docking, and molecular dynamics simulations
Ankylosing spondylitis (AS) is a rheumatic disease that causes inflammation and bone formation in the spine. Despite significant advances in...
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GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases
Knowledge bases have been instrumental in advancing biological research, facilitating pathway analysis and data visualization, which are now widely...
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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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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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Deciphering neuroprotective mechanism of nitroxoline in cerebral ischemia: network pharmacology and molecular modeling-based investigations
Cerebral ischemia is one of the major causes of death and disability worldwide. Currently, existing approved therapies are based on reperfusion and...
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Quantitative phosphoproteomics reveals molecular pathway network in wheat resistance to stripe rust
Protein phosphorylation plays an important role in immune signaling transduction in plant resistance to pathogens. Wheat stripe rust, caused by Puccini...
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Unraveling the anti-breast cancer activity of Cimicifugae rhizoma using biological network pathways and molecular dynamics simulation
Cimicifugae is a commonly used treatment for breast cancer, but the specific molecular mechanisms underlying its effectiveness remain unclear. In...
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Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia
Scientific research has demonstrated that Tinospora cordifolia acts as an anti-aging agent in several experimental models, generating global interest...
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A multimodal graph neural network framework for cancer molecular subtype classification
BackgroundThe recent development of high-throughput sequencing has created a large collection of multi-omics data, which enables researchers to...
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CAT-DTI: cross-attention and Transformer network with domain adaptation for drug-target interaction prediction
Accurate and efficient prediction of drug-target interaction (DTI) is critical to advance drug development and reduce the cost of drug discovery....
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Emerging landscape of molecular interaction networks: Opportunities, challenges and prospects
Network biology finds application in interpreting molecular interaction networks and providing insightful inferences using graph theoretical analysis...
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Dynamic molecular network analysis of iPSC-Purkinje cells differentiation delineates roles of ISG15 in SCA1 at the earliest stage
Better understanding of the earliest molecular pathologies of all neurodegenerative diseases is expected to improve human therapeutics. We...
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Molecular mechanism of Rhubarb in the treatment of non-small cell lung cancer based on network pharmacology and molecular docking technology
Non-small cell lung cancer (NSCLC) is one of the leading causes of death in the world. Rhubarb, a traditional Chinese medicine, has been widely used...
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Systematic analysis on the mechanism of Zhizi-Bopi decoction against hepatitis B via network pharmacology and molecular docking
Purpose: Zhizi-Bopi decoction (ZZBPD) is a classic herbal formula with wide clinical applications in treating liver diseases including hepatitis B....
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Exploration of the molecular mechanism of tea polyphenols against pulmonary hypertension by integrative approach of network pharmacology, molecular docking, and experimental verification
Pulmonary hypertension, a common complication of chronic obstructive pulmonary disease, is a major global health concern. Green tea is a popular...
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HeteroTCR: A heterogeneous graph neural network-based method for predicting peptide-TCR interaction
Identifying interactions between T-cell receptors (TCRs) and immunogenic peptides holds profound implications across diverse research domains and...
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Molecular mechanism of Acanthopanax senticosus in the treatment of Alzheimer’s disease based on network pharmacology and molecular docking
Alzheimer's disease is the most common neurodegenerative disease. Acanthopanax senticosus , also known as Ciwujia or Siberian ginseng in Chinese, has...
