Related papers: Geometrical comparison of two protein structures u…
In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…
Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior and properties of condensed matter systems. While standard quantities for characterizing structure exist,…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
Many algorithms for the computation of correspondences between deformable shapes rely on some variant of nearest neighbor matching in a descriptor space. Such are, for example, various point-wise correspondence recovery algorithms used as a…
A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic…
Determining whether two particle systems are similar is a common problem in particle simulations. When the comparison should be invariant under permutations, orthogonal transformations, and translations of the systems, special techniques…
Feature matching is a challenging computer vision task that involves finding correspondences between two images of a 3D scene. In this paper we consider the dense approach instead of the more common sparse paradigm, thus striving to find…
Finding correspondences between 3D shapes is a crucial problem in computer vision and graphics, which is for example relevant for tasks like shape interpolation, pose transfer, or texture transfer. An often neglected but essential property…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
It is shown how a physical function, namely the Wigner function, that in principle may be measured, can be used to evaluate divergent series.
Shape-similarity between molecules is a tool used by chemists for virtual screening, with the goal of reducing the cost and duration of drug discovery campaigns. This paper reports an entirely novel shape descriptor as an alternative to the…
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…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
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…
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 paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the $C_{\alpha}$-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
A unified method for extracting geometric shape features from binary image data using a steady state partial differential equation (PDE) system as a boundary value problem is presented in this paper. The PDE and functions are formulated to…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…