Free energy calculations are central to understanding the structure, dynamics and function
of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded …

Molecular dynamics simulation is a powerful computational technique to study biomolecular
systems, which complements experiments by providing insights into the structural dynamics …

Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW
domain, was simulated via accelerated molecular dynamics (aMD). In comparison with …

Abstract The Ca 2+-sensing receptor (CaSR) regulates the calcium homeostasis in the
human body via sensing fluctuations in the extracellular Ca 2+ concentration. Naturally …

Many problems studied via molecular dynamics require accurate estimates of various
thermodynamic properties, such as the free energies of different states of a system, which in …

deMon2k is a readily available program specialized in Density Functional Theory (DFT)
simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review …

Background Accelerated molecular dynamics (aMD) has been proven to be a powerful
biasing method for enhanced sampling of biomolecular conformations on general-purpose …

Alchemical free energy calculations using conventional molecular dynamics and
thermodynamic integration rely on simulations performed at fixed values of the coupling …

The relation of surface polarity and conformational preferences is decisive for cell
permeability and thus bioavailability of macrocyclic drugs. Here, we employ grid …

Functional positive cooperative activation of the extracellular calcium ([Ca 2+] o)-sensing
receptor (CaSR), a member of the family CG protein-coupled receptors, by [Ca 2+] o or …