Related papers: Lattice model of protein conformations
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20 letter lattice model of proteins which, relying only on the…
Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible…
We investigate a Kac-type many particle model that allows a reference-free description of plastic deformation. In the framework of the model a solid body is described by a set of particle positions. A lattice is fitted to the particle…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
The Embedded-Atom Model (EAM) provides a phenomenological description of atomic arrangements in metallic systems. It consists of a configurational energy depending on atomic positions and featuring the interplay of two-body atomic…
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…
We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural…
We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are…
A lattice model for binary mixture of lipids and water is introduced and investigated. The orientational degrees of freedom of the amphiphilic molecules are taken into account in the same way as in the model for oil-water-surfactant…
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…
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
Qualitative attributes of the region between order and disorder are examined to explore models of genetic and protein networks. Results show how the connectivity of vertices and the strength of their connections are related and how their…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…