Related papers: Statistical properties of contact vectors
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they…
The dependence of the scaling properties of the structure factor on space dimensionality, range of interaction, initial and final conditions, presence or absence of a conservation law is analysed in the framework of the large-N model for…
Face-to-face social contacts are potentially important transmission routes for acute respiratory infections, and understanding the contact network can improve our ability to predict, contain, and control epidemics. Although workplaces are…
We propose a novel technique, termed compact shape trees, for computing correspondences of single-boundary 2-D shapes in O(n2) time. Together with zero or more features defined at each of n sample points on the shape's boundary, the compact…
We interpret the property of having an infinitesimal symmetry as a variational property in certain geometric structures. This is achieved by establishing a one-to-one correspondence between a class of cone structures with an infinitesimal…
On contact manifolds we describe a notion of (contact) finite-type for linear partial differential operators satisfying a natural condition on their leading terms. A large class of linear differential operators are of finite-type in this…
We establish a relation between higher contact-like structures on supermanifolds and the N = 1 super-Poincare group via its superspace realisation. To do this we introduce a vector-valued contact structure, which we refer to as a…
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…
We exemplarily investigate how optical properties of single scatterers in interacting multi-particle systems influence measurable structure factors. Both particles with linear gradients of their scattering length density and core-shell…
For a drop on an incline with small tilt angle or small Bond number, when the contact line is a circle, we show that the retentive force factor is exactly pi/2 at first order in the tilt angle or the Bond number. The retentive force factor…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
An almost contact metric structure is parametrized by a section of an associated homogeneous fibre bundle, and conditions for this to be a harmonic section, and a harmonic map, are studied. These involve the characteristic vector field, and…
This paper describes a technique for analyzing the stochastic structure of the vectorial capacity using moment--generating functions. In such formulation, for an infectious disease transmitted by a vector, we obtain the generating function…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
In this work, we study the correlation between attribute sets and the occurrence of dense subgraphs in large attributed graphs, a task we call structural correlation pattern mining. A structural correlation pattern is a dense subgraph…
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be…
Many materials contain extended defects of nanosize scale, such as dislocations, cracks, pores, polymorphic inclusions, and other embryos of competing phases. When one is interested not in the precise internal structure of a sample with…
Geometric structures on $\mathbb N Q$-manifolds, i.e.~non-negatively graded manifolds with an homological vector field, encode non-graded geometric data on Lie algebroids and their higher analogues. A particularly relevant class of…