相关论文: Modeling Protein Contact Networks

Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior…

It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…

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…

Protein Contact Network (PCN) is a powerful tool for analysing the structure and function of proteins. In particular, PCN has been used for disclosing the molecular features of allosteric regulation through PCN clustering. Such analysis is…

Self-avoiding random walks were performed on protein residue networks. Compared with protein residue networks with randomized links, the probability of a walk being successful is lower and the length of successful walks shorter in…

A number of recent studies have focused on the statistical properties of networked systems such as social networks and the World-Wide Web. Researchers have concentrated particularly on a few properties which seem to be common to many…

The percolation properties of clustered networks are analyzed in detail. In the case of weak clustering, we present an analytical approach that allows to find the critical threshold and the size of the giant component. Numerical simulations…

Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…

Network topologies can be non-trivial, due to the complex underlying behaviors that form them. While past research has shown that some processes on networks may be characterized by low-order statistics describing nodes and their neighbors,…

Real complex systems are not rigidly structured; no clear rules or blueprints exist for their construction. Yet, amidst their apparent randomness, complex structural properties universally emerge. We propose that an important class of…

The line graphs are clustered and assortative. They share these topological features with some social networks. We argue that this similarity reveals the cliquey character of the social networks. In the model proposed here, a social network…

In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…

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…

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…

The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…

Each complex network (or class of networks) presents specific topological features which characterize its connectivity and highly influence the dynamics of processes executed on the network. The analysis, discrimination, and synthesis of…

Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…

Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…

Large-scale human social network structure is typically inferred from digital trace samples of online social media platforms or mobile communication data. Instead, here we investigate the social network structure of a complete population,…