Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to the simplicity of the setup and parallel granularity of the runs. However, so far, the computational cost limited the estimation of the free energy typically over just a few pullings, thus impeding the evaluation of st...

TRPM7/ChaK1 is a recently discovered atypical protein kinase that has been suggested to selectively phosphorylate the substrate residues located in alpha-helices. However, the actual structure of kinase-substrate complex has not been determined experimentally and the recognition mechanism remains unknown. In this work we explored possible kinase-substrate binding modes and the likelihood of an ...

In this work, the thermal reaction of aluminum (Al) and nickel oxide (NiO) was investigated by molecular dynamics simulations. Some effective features of reaction such as reaction temperature, the reaction mechanism, and diffusion rate of oxygen into aluminum structure were studied. ReaxFF force field was performed to study the Al/NiO thermite reaction behavior at five different temperatures (5...

Titin, a 1-microm-long protein found in striated muscle myofibrils, possesses unique elastic and extensibility properties in its I-band region, which is largely composed of a PEVK region (70% proline, glutamic acid, valine, and lysine residue) and seven-strand beta-sandwich immunoglobulin-like (Ig) domains. The behavior of titin as a multistage entropic spring has been shown in atomic force mic...

About 15 years ago, the steered molecular dynamics (SMD) was used to probe binding of ligand to biomolecule surfaces but in terms of drug design this approach has only recently attached attention of researchers. The main idea of using SMD to screen out leads is based on the hypothesis that the larger is the force needed to unbind a ligand from a receptor the higher its binding affinity. Thus, i...