Proteins are structural and functional components of cells. They interact with each other to drive specific cellular functions. The physical and functional protein interactions are an important feature of cellular organization and regulation. Protein interactions are represented as a network or a graph in which proteins are nodes, and interactions between them are edges. Perturbations in the network affecting essential or central proteins can have pathological consequences. Network or graph theory is a branch of mathematics that provides a conceptual framework to decipher topologically important proteins in the network. These concepts are known as centrality measures. This chapter introduces various centrality metrics and provides a stepwise protocol to quantify protein's strategic positions in the network using an R programming language.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-0716-3327-4_34 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
PHIStruct: Improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings.
Bioinformatics
January 2025
Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, 1004, Philippines.
Motivation: Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.
Results: We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera.
EnrichRBP: an automated and interpretable computational platform for predicting and analyzing RNA-binding protein events.
Bioinformatics
January 2025
School of Artificial Intelligence, Jilin University, Jilin, China.
Motivation: Predicting RNA-binding proteins (RBPs) is central to understanding post-transcriptional regulatory mechanisms. Here, we introduce EnrichRBP, an automated and interpretable computational platform specifically designed for the comprehensive analysis of RBP interactions with RNA.
Results: EnrichRBP is a web service that enables researchers to develop original deep learning and machine learning architectures to explore the complex dynamics of RNA-binding proteins.
The Stenotrophomonas maltophilia L2 cephalosporinase is one of two beta-lactamases which afford S. maltophilia beta-lactam resistance. With the overuse of beta-lactams, selective pressures have contributed to the evolution of these proteins, generating proteins with an extended spectrum of activity.
View Article and Find Full Text PDFRegenerative Functions of Regulatory T Cells and Current Strategies Utilizing Mesenchymal Stem Cells in Immunomodulatory Tissue Regeneration.
Tissue Eng Regen Med
January 2025
Department of Biomedical Engineering, Dongguk University, Seoul, South Korea.
Background: Regulatory T cells (Tregs) are essential for maintaining immune homeostasis and facilitating tissue regeneration by fostering an environment conducive to tissue repair. However, in damaged tissues, excessive inflammatory responses can overwhelm the immunomodulatory capacity of Tregs, compromising their functionality and potentially hindering effective regeneration. Mesenchymal stem cells (MSCs) play a key role in enhancing Treg function.
View Article and Find Full Text PDFThe immune-related gene CD5 is a prognostic biomarker associated with the tumor microenvironment of breast cancer.
Discov Oncol
January 2025
Graduate School of Qinghai University, Xining, 810000, Qinghai Province, People's Republic of China.
The occurrence and progression of breast cancer (BCa) are complex processes involving multiple factors and multiple steps. The tumor microenvironment (TME) plays an important role in this process, but the functions of immune components and stromal components in the TME require further elucidation. In this study, we obtained the RNA-seq data of 1086 patients from The Cancer Genome Atlas (TCGA) database.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!