Related papers: Random close packing in protein cores
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
In protein structure analysis, the accurate characterization of secondary structure elements is crucial for understanding protein function and dynamics. This paper presents a software system designed for the comprehensive analysis of the…
The most efficient way to pack equally sized spheres isotropically in 3D is known as the random close packed state, which provides a starting point for many approximations in physics and engineering. However, the particle size distribution…
Predicting the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year…
Finite mixture models are fitted to spherical data. Kent distributions are used for the components of the mixture because they allow considerable flexibility. Previous work on such mixtures has used an approximate maximum likelihood…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We apply a recent one-dimensional algorithm for predicting random close packing fractions of polydisperse hard spheres [Farr and Groot, J. Chem. Phys. 133, 244104 (2009)] to the case of lognormal distributions of sphere sizes and mixtures…
The structural properties of dense random packings of identical hard spheres (HS) are investigated. The bond order parameter method is used to obtain detailed information on the local structural properties of the system for different…
The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of $v_{CP}…
Emerging coherent X-ray scattering patterns of single particles have shown dominant morphological signatures in agreement with predictions of the scattering model used for conventional protein crystallography. The key question is if and to…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
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…
Single particle diffraction imaging experiments at free-electron lasers (FEL) have a great potential for structure determination of reproducible biological specimens that can not be crystallized. One of the challenges in processing the data…
Studies of random close packing of spheres have advanced our knowledge about the structure of systems such as liquids, glasses, emulsions, granular media, and amorphous solids. When these systems are confined their structural properties…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
A random packing of hard particles represents a fundamental model for granular matter. Despite its importance, analytical modeling of random packings remains difficult due to the existence of strong correlations which preclude the…
For many years it had been believed that steric compatibility of helix interfaces could be the source of the observed preference for particular angles between neighbouring helices as emerging from statistical analysis of protein databanks.…
Circles of a single size can pack together densely in a hexagonal lattice, but adding in size variety disrupts the order of those packings. We conduct simulations which generate dense random packings of circles with specified size…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…