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Fractured surfaces carry unique details that can provide an accurate quantitative comparison to support comparative forensic analysis of those fractured surfaces. In this study, a statistical analysis comparison protocol was applied to a…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
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…
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…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
Identifying novel functional protein structures is at the heart of molecular engineering and molecular biology, requiring an often computationally exhaustive search. We introduce the use of a Deep Convolutional Generative Adversarial…
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…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
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…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly.…
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…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
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…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further…
We present some work relating to fractal transformations on masked iterated function systems and demonstrate how well known algorithms for generating fractal transformations can be modifed for these systems. We also demonstrate that these…
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 Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…