Molecular dynamics simulation of Toxin‐Antitoxin (TA) system in Acinetobacter baumannii to explore the novel mechanism for inhibition of cell wall biosynthesis: Zeta Toxin as an effective therapeutic target

2021 ◽  
Author(s):  
Alagesan Karthika ◽  
Balajee Ramachandran ◽  
Jeyarajpandian Chitra ◽  
Dhamodharan Prabhu ◽  
Sundaraj Rajamanikandan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Wall ◽  
Molecular Dynamics Simulation ◽  
Acinetobacter Baumannii ◽  
Therapeutic Target ◽  
Dynamics Simulation ◽  
Cell Wall Biosynthesis ◽  
The Novel

scholarly journals Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2196
Author(s):  
Barış Kurt ◽  
Hamdi Temel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Biologically Active ◽  
Dynamics Simulation ◽  
The Novel ◽  
Ab Initio Method ◽  
Crystallographic Structures ◽  
Dynamics Simulations ◽  
Experimental Structure

Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and using the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.

Plasma-Induced Destruction of Bacterial Cell Wall Components: A Reactive Molecular Dynamics Simulation

2013 ◽  
Vol 117 (11) ◽  
pp. 5993-5998 ◽  
Author(s):  
Maksudbek Yusupov ◽  
Annemie Bogaerts ◽  
Stijn Huygh ◽  
Ramses Snoeckx ◽  
Adri C. T. van Duin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Wall ◽  
Molecular Dynamics Simulation ◽  
Bacterial Cell ◽  
Bacterial Cell Wall ◽  
Dynamics Simulation ◽  
Cell Wall Components ◽  
Reactive Molecular Dynamics ◽  
Wall Components

A comprehensive review on the molecular dynamics simulation of the novel thermal properties of graphene

RSC Advances ◽  
2015 ◽  
Vol 5 (109) ◽  
pp. 89415-89426 ◽  
Author(s):  
Jingchao Zhang ◽  
Fei Xu ◽  
Yang Hong ◽  
Qingang Xiong ◽  
Jianming Pan
Keyword(s):  
Molecular Dynamics ◽  
Thermal Properties ◽  
Molecular Dynamics Simulation ◽  
State Of The Art ◽  
Dynamics Simulation ◽  
The Novel ◽  
Comprehensive Review

This review summarizes state-of-the-art progress in the molecular dynamics simulation of the novel thermal properties of graphene.

Sign in / Sign up

Export Citation Format

Share Document