Related papers: Atomic Density Distributions in Proteins: Structur…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
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 beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
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 present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
A double-index atomic partitioning of the molecular first-order density matrix is proposed. Contributions diagonal in the atomic indices correspond to atomic density matrices, whereas off-diagonal contributions carry information about the…
The similarity between protein sequences is a directly and easly computed quantity from which to deduce information about their evolutionary distance and to detect homologous proteins. The SIMAP database -- Similarity Matrix of Proteins --…
Motivation: Human cancer is caused by the accumulation of somatic mutations in tumor suppressors and oncogenes within the genome. In the case of oncogenes, recent theory suggests that there are only a few key "driver" mutations responsible…
The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the folded states, whose interiors are densely packed, the radii of…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
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…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
We analyzed folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory for 28 two-state proteins. The scaling exponent ranged from 0.2 to 0.45 with an average of 0.33. This average…
The distribution of amino acid along the protein sequences plays an imperative role in facilitating different biological functions. Currently, there is insufficient scientific data, which represents the arrangement of amino acid in the…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Eficient, physically-inspired descriptors of the structure and composition of molecules and materials play a key role in the application of machine-learning techniques to atomistic simulations. The proliferation of approaches, as well as…