in this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. from a pdb blast search, the selected haloalkane dehalogenase (pdb code: 1ede) had a close structural homology with a lucifearse (pdb code: 2psj chain a) sharing an identity of 33%. initially, the amino...

Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of...

This paper describes BioPAUÁ project first release of a portal for Molecular Dynamics (MD) using a computational grid environment. It unites MD simulations and analyses tools with grid technologies to provide support to biomolecular structures in silico experiments. BioPAUÁ Project goal is to offer a tool, as well the facility, for researches working in several important fields (e.g., bioinform...

The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity. Starting from the open crystal structures, we have studied the gating mechanism of these channels by mol...

Anhydrous Hydrogen Fluoride (HF) at high temperatures and pressures is used to process manufacture nuclear fuel. As HF often directly with uranium, correct neutron thermal scattering cross sections are crucial criticality safety applications. Classical molecular dynamics (CMD) simulation of the flexible system was create law (TSL) sections. The initial 2-site model in LAMMPS, it can not capture...

Background & Aims: The normal form of the prion protein is called PrPC and its infectious form is called PrPSc. This protein functions like a crystallized core for the transformation of PrPc into an abnormal PrPSc. The aim of the present study was to investigate the effect of temperature on human prion protein structure through molecular dynamic simulation. Methods: In this research, the GROMAC...

Microtubules, the active filaments with tubular shapes, play important roles in a wide range of cellular functions, including structural supports, mitosis, cytokinesis, and vesicular transport, which are essential for the growth and division of eukaryotic cells. Finding properties of microtubules is one of the main concerns of scientists. This work helps to obtain mechanical properties of m...