Related papers: Identification of Human Proteins vulnerable to mul…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Although cancer is known to be characterized by several unifying biological hallmarks, systems biology has had limited success in identifying molecular signatures present in in all types of cancer. The current availability of rich data sets…
PEBPs (PhosphatidylEthanolamine Binding Proteins) form a protein family widely present in the living world since they are encountered in microorganisms, plants and animals. In all organisms PEBPs appear to regulate important mechanisms that…
Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. However, only 4% of PPIs are annotated with PTMs in biological knowledge databases such as IntAct, mainly performed…
The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices…
Research in bioinformatics is a complex phenomenon as it overlaps two knowledge domains, namely, biological and computer sciences. This paper has tried to introduce an efficient data mining approach for classifying proteins into some useful…
Genes/Proteins do not work alone within our body, rather as a group they perform certain activities indicated as pathways. Signalling transduction pathways (STPs) are some of the important pathways that transmit biological signals from…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Drug discovery remains time-consuming, labor-intensive, and expensive, often requiring years and substantial investment per drug candidate. Predicting compound-protein interactions (CPIs) is a critical component in this process, enabling…
One of the most challenging problems in biomedicine and genomics is the identification of disease biomarkers. In this study, proteomics data from seven major cancers were used to construct two weighted protein-protein interaction (PPI)…
Protein-protein interactions drive many biological processes, including the detection of phytopathogens by plants' R-Proteins and cell surface receptors. Many machine learning studies have attempted to predict protein-protein interactions…
Breast cancer's complexity and variability pose significant challenges in understanding its progression and guiding effective treatment. This study aims to integrate protein sequence data with expression levels to improve the molecular…
Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods…
It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human…
In this study, we introduced a new unit, named "protein token", as a dynamic protein structural unit for protein-protein interactions. Unlike the conventional structural units, protein token is not based on the sequential or spatial…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
Accurate information about protein content in the organism is instrumental for a better understanding of human biology and disease mechanisms. While the presence of certain types of proteins can be life-threatening, the abundance of others…