Related papers: Functional geometry of protein-protein interaction…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Protein-protein interaction (PPI) networks provide valuable insights into the function of biological systems, and aligning multiple PPI networks can reveal important functional relationships between different species. However, assessing the…
A number of network structural characteristics have recently been the subject of particularly intense research, including degree distributions, community structure, and various measures of vertex centrality, to mention only a few. Vertices…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
Simplicial complexes are gaining increasing scientific attention as they are generalized network structures that can represent the many-body interactions existing in complex systems raging from the brain to high-order social networks.…
Protein-protein interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has…
Higher-order networks are widely used to describe complex systems in which interactions can involve more than two entities at once. In this paper, we focus on inclusion within higher-order networks, referring to situations where specific…
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and…
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry.…
Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the…
Simplicial complexes are a generalization of graphs that model higher-order relations. In this paper, we introduce simplicial patterns -- that we call simplets -- and generalize the task of frequent pattern mining from the realm of graphs…
One of the most difficult problems difficult problem in systems biology is to discover protein-protein interactions as well as their associated functions. The analysis and alignment of protein-protein interaction networks (PPIN), which are…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Protein-protein interactions (PPIs) perform important roles on biological functions. Researches of mutants on protein interactions can further understand PPIs. In the past, many researchers have developed databases that stored mutants on…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
This paper presents the foundational ideas for a new way of modeling social aggregation. Traditional approaches have been using network theory, and the theory of random networks. Under that paradigm, every social agent is represented by a…
Many real networks in social sciences, biological and biomedical sciences or computer science have an inherent structure of simplicial complexes reflecting many-body interactions. Therefore, to analyse topological and dynamical properties…