Related papers: Statistical properties of contact vectors
This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented…
Connecting curves have been shown to organize the rotational structure of strange attractors in three-dimensional dynamical systems. We extend the description of connecting curves and their properties to higher dimensions within the special…
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…
Species interaction networks are a powerful tool for describing ecological communities; they typically contain nodes representing species, and edges representing interactions between those species. For the purposes of drawing abstract…
Properties of several sorts of lattices of convex subsets of R^n are examined. The lattice of convex sets containing the origin turns out, for n>1, to satisfy a set of identities strictly between those of the lattice of all convex subsets…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
In this letter, a novel method for change detection is proposed using neighborhood structure correlation. Because structure features are insensitive to the intensity differences between bi-temporal images, we perform the correlation…
In human and animal groups, social interactions often rely on the transmission of information via visual observation of the behavior of others. These visual interactions are governed by the laws of physics and sensory limits. Individuals…
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…
Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range…
We have considered the problem of protein design based on a model where the contact energy between amino acid residues is fitted phenomenologically using the Miyazawa--Jernigan matrix. Due to the simple form of the contact energy function,…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
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…
It was found that the isoscalar-scalar and isovector-scalar mesons play significant roles in nuclear matter physics. However, the underlying structures of these resonances are not yet well understood. We construct a three-flavor baryonic…
Motivated by recent experiments, we investigate the scattering properties of percolation clusters generated by numerical simulations on a three dimensional cubic lattice. Individual clusters of given size are shown to present a fractal…
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…
The ratio of the static matter structure factor measured in experiments on coherent X-ray scattering to the static structure factor measured in experiments on neutron scattering is considered. It is shown theoretically that this ratio in…
The measurement of the similarity of RNA secondary structures, and in general of contact structures, of a fixed length has several specific applications. For instance, it is used in the analysis of the ensemble of suboptimal secondary…
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…
RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the…