Related papers: Statistical properties of contact vectors
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Previous studies have claimed that there exist correlations among certain nuclear saturation parameters and neutron star observables, such as the slope of the symmetry energy and the radius of a $1.4M_{\odot}$ neutron star. However, it is…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
For machines to interact with the physical world, they must understand the physical properties of objects and materials they encounter. We use fabrics as an example of a deformable material with a rich set of mechanical properties. A thin…
In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement…
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…
Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
We introduce the vector meson $\omega$ into the Quark Meson model, and study the impact of vector interactions on the properties of static hadrons using the mean-field approximation. The short-range repulsive force associated with vector…
Developing an accurate scoring function is essential for successfully predicting protein structures. In this study, we developed a statistical potential function, called OPUS-Beta, for energetically evaluating beta-sheet contact pattern…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Two types of average structures of a single knotted ring polymer are studied by Brownian dynamics simulations. For a ring polymer with N segments, its structure is represented by a 3N -dimensional conformation vector consisting of the…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Classically, the quantity of contact area $A_R$ between two bodies is considered a proxy for the force of friction. However, bond density across the interface - quality of contact - is also relevant, and contemporary debate often centers…
Using small-angle neutron scattering and liquid integral equation theory, we relate the structure factor of flexible dendrimers of 4th generation to their average shape. The shape is measured as a radial density profile of monomers…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…