Related papers: Computation of protein geometry and its applicatio…
A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…
In this video we highlight the application of Computational Geometry to our understanding of the formation and dynamics of the Cosmic Web. The emergence of this intricate and pervasive weblike structure of the Universe on Megaparsec scales…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
We use density functional theory to describe the phase behaviors of rigid molecules. The construction of kernel function G(x, P, x, P) is discussed. Excluded-volume potential is calculated for two types of molecules with C_{2v} symmetry.…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
We introduce a new, simplified model of proteins, which we call protein metastructure. The metastructure of a protein carries information about its secondary structure and $\beta$-strand conformations. Furthermore, protein metastructure…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
The paper describes a new algorithm of construction of the nonlinear arithmetic triangle on the basis of numerical simulation and the binary system. It demonstrates that the numbers that fill the nonlinear arithmetic triangle may be…
Many physical systems can be studied as collections of particles embedded in space, evolving through deterministic evolution equations. Natural questions arise concerning how to characterize these arrangements - are they ordered or…
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…
Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
A method is proposed for the characterisation of the entropy of cellular structures, based on the compactivity concept for granular packings. Hamiltonian-like volume functions are constructed both in two and in three dimensions, enabling…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
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…
We present a new and simple randomized algorithm for constructing the Delaunay triangulation using nearest neighbor graphs for point location. Under suitable assumptions, it runs in linear expected time for points in the plane with…
Voronoi tessellations have been used to model the geometric arrangement of cells in morphogenetic or cancerous tissues, however so far only with flat hypersurfaces as cell-cell contact borders. In order to reproduce the experimentally…
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that…