相关论文: On universal aspects of the left-handed helix regi…

Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe…

We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry.…

We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…

Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…

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 structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to…

The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…

Local protein structure analysis is informative to protein structure analysis and has been used successfully in protein structure prediction and others. Proteins have recurring structural features, such as helix caps and beta turns, which…

We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…

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 chain of algebraic geometry constructions permits to transfer from the minimal surface with zero instability index, and from the lattice over the ring of cyclotomic integers to the tetra-block helix. The tetra-block is the 7-vertex…

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…

The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…

A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…

The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…

The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…

We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid and has the Ramachandran…

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…

Although recent spectroscopic studies of chemically denatured proteins hint at significant nonrandom residual structure, the results of extensive small angle X-ray scattering studies suggest random coil behavior, calling for a coherent…