Related papers: Comparative analysis of protein structure using mu…
Structural relationships among proteins are important in the study of their evolution as well as in drug design and development. The protein 3D structure has been shown to be effective with respect to classifying proteins. Prior work has…
In this review we identify a new category of structural optimization methods that has emerged over the last 20 years, which we propose to call feature-mapping methods. The two defining aspects of these methods are that the design is…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
We present a novel method for characterizing the microstructure of a material from volumetric datasets such as 3D image data from computed tomography (CT). The method is based on a new statistical model for the distribution of voxel…
Protein fold classification is a classic problem in structural biology and bioinformatics. We approach this problem using persistent homology. In particular, we use alpha shape filtrations to compare a topological representation of the data…
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…
Significant developments in the field of additive manufacturing (AM) allowed the fabrication of complex microarchitectured components with varying porosity across different scales. However, due to the high complexity of this process, the…
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…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
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…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
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…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
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…
The basic problem of shape complementarity analysis appears fundamental to applications as diverse as mechanical design, assembly automation, robot motion planning, micro- and nano-fabrication, protein-ligand binding, and rational drug…
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 paper, we derive new shape descriptors based on a directional characterization. The main idea is to study the behavior of the shape neighborhood under family of transformations. We obtain a description invariant with respect to…
In previous work, we introduced a method for modeling a configuration of objects in 2D and 3D images using a mathematical "medial/skeletal linking structure." In this paper, we show how these structures allow us to capture positional…