Related papers: Network properties of protein structures
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
The capacity to resist attacks from the environment is crucial to the survival of all organisms. We quantitatively analyze the susceptibility of protein interaction networks of numerous organisms to random and malicious attacks. We find for…
We propose a network model with a fixed number of nodes and links with a dynamics which favors links between nodes differing in connectivity. Parameter regimes where the degree distributions follow power-laws, P(k) ~ k^-gamma, high…
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…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Networks describing the interaction of the elements that constitute a complex system grow and develop via a number of different mechanisms, such as the addition and deletion of nodes, the addition and deletion of edges, as well as the…
It has been discovered recently that many social, biological and ecological systems have the so-called small-world and scale-free features, which has provoked new research interest in the studies of various complex networks. Yet, most…
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
The network characteristics based on the phonological similarities in the lexicons of several languages were examined. These languages differed widely in their history and linguistic structure, but commonalities in the network…
In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological…
The arrangements of particles and forces in granular materials have a complex organization on multiple spatial scales that ranges from local structures to mesoscale and system-wide ones. This multiscale organization can affect how a…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…