Related papers: PDBCirclePlot: A Novel Visualization Method for Pr…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale.…
X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, and dual polarization interferometry, etc are indeed very powerful tools to determine the 3D structures of proteins (including the membrane proteins), though they are…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using…
Visual object tracking is a significant computer vision task which can be applied to many domains such as visual surveillance, human computer interaction, and video compression. In the literature, researchers have proposed a variety of 2D…
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 study of moving particles (e.g. molecules, virus, vesicles, organelles, or whole cells) is crucial to decipher a plethora of cellular mechanisms within physiological and pathological conditions. Powerful live-imaging approaches enable…
This study introduces a new method of visualizing complex tree structured objects. The usefulness of this method is illustrated in the context of detecting unexpected features in a data set of very large trees. The major contribution is a…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
In this paper, we introduce the cyclic polygon plot, a representation based on a novel projection concept for multi-dimensional values. Cyclic polygon plots combine the typically competing requirements of quantitativeness, image-space…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
Multidimensional scaling allows visualizing high-dimensional data as 2D maps with the premise that insights in 2D reveal valid information in high-dimensions. However, the resulting projections suffer from artifacts such as bad local…
Medical visualization is the use of computers to create 3D images from medical imaging data sets, almost all surgery and cancer treatment in the developed world relies on it.Volume visualization techniques includes iso-surface…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physico-chemical…