Acetylcholinesterase (AChE) enzyme which catalyses the hydrolysis of choline esters, such as acetylcholine, is very important in nerve function. Previous structural studies showed the possible amyloid fibril formation on the AChE. Therefore it is important to understand interaction of ligands to prevent the formation of  amyloid fibrils. The purpose of the present study was to  char...

Renewable energy will play a crucial role in the future society of the 21st century. The various renewable energy sources need to be balanced and their use carefully planned since they are characterized by high temporal and spatial variability that will pose challenges to maintaining a well balanced supply and to the stability of the grid. This article examines the ways that future 'energy land...

UNLABELLED From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the a...

Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to decrease the activation energy between various local energy minima smoothing the energy landscape, rescuing misfolded proteins from conformational traps and s...

We present a method for approximating a tness landscape as a superposition of elementary landscapes Given a correlation function of the landscape in question we show that the relative amplitudes of contributions with p ary interactions can be computed We show an application to RNA free energy landscapes

The functional sites were predicted for Nudix enzymes from pathogenic microorganisms such as Streprococcus pneumonia (2B06) and Enterococcus faecalis (2AZW). Their structures are already determined, however, no data is reported about their functional sites, substrates and inhibitors. Therefore, we report prediction of functional sites in these Nudix enzymes via Geometric Invariant (GI) techniqu...

Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure-based computer-aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently ...

Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only...