相关论文: Intramolecular Structure of Proteins as driven by …
The application of optimization techniques derived from the study of Euclidean full Steiner Trees to macromolecules like proteins is reported in the present work. We shall use the concept of Euclidean Steiner Ratio Function (SRF) as a good…
In this work, I collect and discuss a series of open questions in one-dimensional geometric optimization in Euclidean spaces. The focus is on two classes of problems: maximal distance minimizers and Steiner trees. Maximal distance…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
The Euclidean Steiner tree problem, normally posed in two dimensions, seeks to connect a set of prescribed terminal nodes by placing additional nodes, known as Steiner points, with edges connecting such nodes either to another Steiner point…
Modern approaches to the search of Relative and Global minima of potential energy function of Biomacromolecular structures include techniques of combinatorial optimization like the study of Steiner Points and Steiner Trees. These methods…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA.…
Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
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…
We describe a technique to reorganize topologies of Steiner trees by exchanging neighbors of adjacent Steiner points. We explain how to use the systematic way of building trees, and therefore topologies, to find the correct topology after…
In the Euclidean Steiner Tree problem, we are given as input a set of points (called terminals) in the $\ell_2$-metric space and the goal is to find the minimum-cost tree connecting them. Additional points (called Steiner points) from the…
The Euclidean Steiner problem is the problem of finding a set $St$, with the shortest length, such that $St \cup A$ is connected, where $A$ is a given set in a Euclidean space. The solutions $St$ to the Steiner problem will be called…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
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…
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…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…