Nagashima U. – TechConnect Briefs

REMD toolkit : A Composable Software to Generate Parallelized Simulation Programs

We developed a toolkit to generate a replica exchange method program which is suitable to solve the multiple-minima problem that prevents the accurate estimation of thermodynamical quantities. The toolkit was designed as a set of [...]

DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method -Implementation of SCF Convergence-

Watanabe T., Inadomi Y., Tanaka S., Nagashima U., National Institute of Advanced Industrial and Science and Technology, JP

The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic [...]

Molecular Simulation of DNA Microarrays – an Application of 2D particle mesh Ewald algorithm

Watanabe T., Kawata M., Nagashima U., National Institute of Advanced Industrial and Science and Technology, JP

We have developed the two-dimensional particle mesh Ewald (2D-PME) algorithm for molecular dynamics (MD) simulation, and applied it to have knowledge of the behavior of DNA and its interaction on microarrays, which crucial in the [...]

Fast, Accurate Molecular Dynamics Simulations for Surfaces and Membranes

Kawata M., Nagashima U., National Institute of Advanced Industrial Science and Technology, JP

We have developed new fast method for calculating the accurate Coulomb interactions for quasi-2D systems and implemented in the MD calculations. We present the details of the computational steps to implement the 2D-PME method, focusing [...]

Replica Exchange Molecular Dynamics Toolkit for Drug-receptor Docking

Ito M., Nishikawa T., Nagashima U., National Institute of Advanced Industrial Science and Technology, JP

In this post-genomic era, much attention is focused on the 3D structure and flexibility of protein molecules for the rational drug design. Although the structure information provides a good starting point for estimating the ligand-protein [...]

CONFLEX: Conformational Behaviors of Polypeptides as Predicted by a Conformational Space Search

Goto H., Takahashi T., Takata Y., Ohta K., Nagashima U., Toyohashi University of Technology, JP

The elucidation of the stable conformations and the folding process of proteins is one of the most fundamental and challenging goals in life science. While some of the most common secondary structures (e.g., a few [...]