Markov state models have become very popular for the description of conformation dynamics of molecules over long timescales. The construction of such models requires a partitioning of the configuration space such that the discretization can serve as an approximation of metastable conformations. Since the computational complexity for the construction of a Markov state model increases quadratical...

UNLABELLED Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input ...

Predicting native conformations of a protein sequence is known as de novo structure prediction and is a central challenge in computational biology. Most computational protocols employ Monte Carlo sampling. Evolutionary search algorithms have also been proposed to enhance sampling of near-native conformations. These approaches bias stochastic search by an energy function, even though current ene...

A protein molecule assumes specific conformations under native conditions to fit and interact with other molecules. Due to the role that three-dimensional structure plays in protein function, significant efforts are devoted to elucidating native conformations. Many search algorithms are proposed to navigate the high-dimensional protein conformational space and its underlying energy surface in s...

Quantitative Structure-Selectivity Relationships (QSSR) are developed for a library of 40 phase-transfer asymmetric catalysts, based around quaternary ammonium salts, using Comparative Molecular Field Analysis (CoMFA) and closely related variants. Due to the flexibility of these catalysts, we use molecular dynamics (MD) with an implicit Generalized Born solvent model to explore their conformati...

The structure of bacteriophage epsilon15 has recently been determined by 3D reconstruction of single particle cryo-electron microscopy images. Although this study revealed that the viral genome inside the bacteriophage is on average coaxially spooled, individual DNA conformations inside the capsid could not be determined. In the current study, we present the results of 40 independent simulation...

The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the p...

In light of the recent very rapid progress in protein structure prediction, accessing multitude functional states is becoming more central than ever before. Indeed, proteins are flexible macromolecules, and they often perform their function by switching between different conformations. However, high-resolution experimental techniques such as X-ray crystallography cryogenic electron microscopy c...