Related papers: Statistical properties of contact vectors
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
Compartmental models based on tracer mass balance are extensively used in clinical and pre-clinical nuclear medicine in order to obtain quantitative information on tracer metabolism in the biological tissue. This paper is the first of a…
We compute continuum and infinite volume limit extrapolations of the structure factors of neutron matter at finite temperature and density. Using a lattice formulation of leading-order pionless effective field theory, we compute the…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed…
In this paper, we provide a statistical analysis of high-resolution contact pattern data within primary and secondary schools as collected by the SocioPatterns collaboration. Students are graphically represented as nodes in a temporally…
We study the sectional curvature of plane distributions on 3-manifolds. We show that if the distribution is a contact structure it is easy to manipulate this curvature. As a corollary we obtain that for every transversally oriented contact…
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…
Quantifying the relationship between geometric descriptors of microstructure and effective properties like permeability is essential for understanding and improving the behavior of porous materials. In this paper, we employ a previously…
Visual relation detection methods rely on object information extracted from RGB images such as 2D bounding boxes, feature maps, and predicted class probabilities. We argue that depth maps can additionally provide valuable information on…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…
In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…
A contact graph of a packing of closed balls is a graph with balls as vertices and pairs of tangent balls as edges. We prove that the average degree of the contact graph of a packing of balls (with possibly different radii) in…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
Temporal graphs represent interactions between entities over time. Deciding whether entities can reach each other through temporal paths is useful for various applications such as in communication networks and epidemiology. Previous works…