Related papers: Statistical Properties of Contact Maps
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
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…
Contact (or mixing, or more generally connectivity) matrices are a fundamental component of modelling and inference for infectious disease epidemiology. Their structure and parametrisation directly accounts for the frequency of interactions…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
We survey recent results on some one- and two-dimensional patterns generated by random permutations of natural numbers. In the first part, we discuss properties of random walks, evolving on a one-dimensional regular lattice in discrete time…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments…
A protein contact map is a binary symmetric adjacency matrix capturing the distance relationship between atoms of a protein. Each cell (i, j) of a protein contact map states whether the atoms (nodes) i and j are within some Euclidean…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
We estimate the probability regarding polymerization of a macromolecule which is made of distinct monomers. The lattice model of the random walk has been used to mimic the conformations of an ideal chain in two and three dimensions. It has…
Network visualization allows a quick glance at how nodes (or actors) are connected by edges (or ties). A conventional network diagram of "contact tree" maps out a root and branches that represent the structure of nodes and edges, often…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
We obtain the solution of models of self-avoiding walks with attractive interactions on Husimi lattices built with squares. Two attractive interactions are considered: between monomers on first-neighbor sites and not consecutive along a…
Combinatorial enumeration of various RNA secondary structures and protein contact maps, is of great interest for both combinatorists and computational biologists. Enumeration of protein contact maps has considerable difficulties due to the…
Contact matrices provide a coarse grained description of the configuration omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when the distance between the position of the i-th and j-th step are less than or equal to…
Motivated by a problem arising from pharmaceutical science [B. Baeumer et al., Discr. Contin. Dyn. Sys. B 12], we study random walks on the contact graph of a bidisperse random sphere packing. For a random walk on the unweighted graph that…
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…
A mated-CRT map is a random planar map obtained as a discretized mating of correlated continuum random trees. Mated-CRT maps provide a coarse-grained approximation of many other natural random planar map models (e.g., uniform triangulations…