Researchers at the Center for Computational Sciences, University of Tsukuba, have developed an accessible platform to overcome the limitations of conventional static docking simulations, offering new ...

DNA topoisomerase-IA is an essential enzyme that relaxes supercoiled DNA by introducing transient single-strand breaks through a covalent phosphorylated tyrosine (PTR) intermediate. This cleavage ...

Abstract: Since they offer profound insights into the atomic-level interactions between drug candidates and their biological targets, molecular dynamics (MD) simulations have become extremely ...

In this section we will build the system via Leap and run minimization via Sander. Here a brief description of the system and the procedure used to generate the topology and coordinate files. For this ...

CRISP is a post-simulation analysis package built on the Atomic Simulation Environment (ASE). It is designed for efficient and insightful analysis of molecular dynamics (MD) and other simulations, ...

Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator.

Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator. Non-Commercial (NC): Only non-commercial uses of the work are permitted. A complete ...

We study the cavitation bubble that forms as a nano-scale spherical surface is detached from a flat surface using molecular dynamics (MD) simulations. This investigation maps the onset and early ...

Molecular dynamics simulations have emerged as an indispensable tool in modern biomedical research, particularly in the study of protein kinases. This computational approach permits detailed ...

This research area employs molecular dynamics (MD) simulations to unravel the intricate behaviour of molecules at the juncture between vapour and liquid phases. MD simulations provide atomistic ...

The success of a molecular dynamics simulation depends on the accuracy of the force field used to define the atomic interactions. It is challenging to train both classical and modern machine-learning ...

Abstract: The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, ...