Related papers: Virtual reality based approach to protein heavy-at…
Recent advancements in deep learning for predicting 3D protein structures have shown promise, particularly when leveraging inputs like protein sequences and Cryo-Electron microscopy (Cryo-EM) images. However, these techniques often fall…
In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Transmission electron microscopy (TEM) is a potent technique for the determination of three-dimensional atomic scale structure of samples in structural biology and materials science. In structural biology, three-dimensional structures of…
To obtain an electron-density map from a macromolecular crystal the phase-problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitantly the determination of the heavy atom substructure. This is…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Three-dimensional particle reconstruction with limited two-dimensional projections is an under-determined inverse problem that the exact solution is often difficult to be obtained. In general, approximate solutions can be obtained by…
The need for advanced materials has led to the development of complex, multi-component alloys or solid-solution alloys. These materials have shown exceptional properties like strength, toughness, ductility, electrical and electronic…
We propose a method to detect and reconstruct multiple 3D objects from a single RGB image. The key idea is to optimize for detection, alignment and shape jointly over all objects in the RGB image, while focusing on realistic and physically…
This work describes and demonstrates the operation of a virtual X-ray algorithm operating on finite-element post-processing results which allows for higher polynomial orders in geometry representation as well as density distribution. A…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
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…
We present a fast and reliable algorithm that gives precise location of breast tumours for a partial mastectomy. Our algorithm is fully implemented in the Surface Evolver, which is a general-purpose simulator of physical experiments. By…
We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each compound…
Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require.…
Three-dimensional reconstruction of atomic structure, known as atomic electron tomography (AET), has found increasing applications in materials science. The AET has been limited to very small nanoparticles due to the challenges of obtaining…
In high-energy particle collisions, the reconstruction of secondary vertices from heavy-flavour hadron decays is crucial for identifying and studying jets initiated by $b$- or $c$-quarks. Traditional methods, while effective, require…
The present work deals with the formulation of a Virtual Element Method (VEM) for two dimensional structural problems. The contribution is split in two parts: in part I, the elastic problem is discussed, while in part II [3] the method is…