Probing the binding mechanism of novel dual NF-κB/AP-1 inhibitors by 3D-QSAR, docking and molecular dynamics simulations

RSC Advances ◽  
2015 ◽  
Vol 5 (99) ◽  
pp. 81523-81532 ◽  
Author(s):  
Shaojie Ma ◽  
Shepei Tan ◽  
Danqing Fang ◽  
Rong Zhang ◽  
Shengfu Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Computational Study ◽  
3D Qsar ◽  
Structural Features ◽  
Binding Mechanism ◽  
Interaction Mechanisms ◽  
Dynamics Simulations

Potent dual NF-κB/AP-1 inhibitors could effectively treat immunoinflammatory diseases. An integrated computational study was carried out to identify the most favourable binding sites, the structural features and the interaction mechanisms.

Liquid dibromomethane under pressure: a computational study

2021 ◽  
Vol 23 (4) ◽  
pp. 2964-2971
Author(s):  
Bernadeta Jasiok ◽  
Mirosław Chorążewski ◽  
Eugene B. Postnikov ◽  
Claude Millot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Computational Study ◽  
Thermal Expansivity ◽  
Dynamics Simulations ◽  
Isobaric Thermal Expansivity

Thermophysical properties of liquid dibromomethane are investigated by molecular dynamics simulations between 268 and 328 K at pressures up to 3000 bar. Notably, the isotherms of the isobaric thermal expansivity cross around 800 bar.

Cluster, Surface and Bulk Properties of ZnCd Binary Alloys: Molecular-Dynamics Simulations

2005 ◽  
Vol 502 ◽  
pp. 51-56 ◽  
Author(s):  
Sakir Erkoc
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Structural Features ◽  
Bulk Materials ◽  
Bulk Properties ◽  
Atom Clusters ◽  
Dynamics Simulations ◽  
Mixed Clusters ◽  
Stable Structures

The structural and electronic properties of isolated neutral ZnmCdn clusters for m+n £ 3 have been investigated by performing density functional theory calculations at B3LYP level. The optimum geometries, vibrational frequencies, electronic structures, and the possible dissosiation channels of the clusters considered have been obtained. An empirical many-body potential energy function (PEF), which comprices two- and three-body atomic interactions, has been developed to investigate the structural features and energetics of ZnmCdn (m+n=3,4) microclusters. The most stable structures were found to be triangular for the three-atom clusters and tetrahedral for the four-atom clusters. On the other hand, the structural features and energetics of Znn-mCdm (n=7,8) microclusters, and Zn50, Cd50, Zn25Cd25, Zn12Cd38, and Zn38Cd12 nanoparticles have been investigated by performing molecular-dynamics computer simulations using the developed PEF. The most stable structures were found to be compact and three-dimensional for all elemental and mixed clusters. An interesting structural feature of the mixed clusters is that Zn and Cd atoms do not mix in mixed clusters, they come together almost without mixing. Surface and bulk properties of Zn, Cd, and ZnCd systems have been investigated too by performing molecular-dynamics simulations using the developed PEF. Surface reconstruction and multilayer relaxation on clean surfaces, adatom on surface, substitutional atom on surface and bulk materials, and vacancy on surface and bulk materials have been studied extensively.

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