Related papers: New algorithm to determine a minimal representatio…
Modelling, parameter identification, and simulation play an important role in systems biology. Usually, the goal is to determine parameter values that minimise the difference between experimental measurement values and model predictions in…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
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…
Many problems arise in computational biology can be reduced to the minimization of energy function, that determines on the geometry of considered molecule. The solution of this problem allows in particular to solve folding and docking…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
The precise tracking of micron sized colloidal particles - held in the vicinity of each other using optical tweezers - is an elegant way to gain information about the particle-particle pair interaction potential. The accuracy of the method,…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big…
We present a novel particle management method using the Characteristic Mapping framework. In the context of explicit evolution of parametrized curves and surfaces, the surface distribution of marker points created from sampling the…
It is now well accepted that cellular responses to materials in a biological medium reflect greatly the adsorbed biomolecular layer, rather than the material itself. Here, we study by molecular dynamic simulations the competitive protein…
Zernike polynomials are a basis of orthogonal polynomials on the unit disk that are a natural basis for representing smooth functions. They arise in a number of applications including optics and atmospheric sciences. In this paper, we…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
Thinning is the removal of contour pixels/points of connected components in an image to produce their skeleton with retained connectivity and structural properties. The output requirements of a thinning procedure often vary with…
The accurate description of molecule-surface interactions requires a detailed knowledge of the underlying potential-energy surface (PES). Recently, neural networks (NNs) have been shown to be an efficient technique to accurately interpolate…
Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of…
A simple "trick" is proposed, which allows to perform exactly the site-averaging procedure required when developing integral equation theories of interaction site models of macromolecular fluids. It shows that no approximation is involved…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…