scholarly journals Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations

2003 ◽  
Vol 31 (2) ◽  
pp. 629-638 ◽  
Author(s):  
W. Li
Keyword(s):  
Molecular Dynamics ◽  
16S Rrna ◽  
Ribosomal Protein ◽  
Molecular Dynamics Simulations ◽  
Binding Interactions ◽  
Central Domain ◽  
The Core ◽  
Ribosomal Protein S15 ◽  
Dynamics Simulations

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

Biopolymers ◽  
2006 ◽  
Vol 82 (5) ◽  
pp. 504-520 ◽  
Author(s):  
Kamila Réblová ◽  
Filip Lankas̆ ◽  
Filip Rázga ◽  
Maryna V. Krasovska ◽  
Jaroslav Koc̆a ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
16S Rrna ◽  
Molecular Dynamics Simulations ◽  
Structure Dynamics ◽  
Dynamics Simulations

A MOLECULAR MODELING STUDY OF GENERATION-DEPENDENT STABILITY OF DENDRITIC POLYSILANES

2008 ◽  
Vol 07 (05) ◽  
pp. 923-931 ◽  
Author(s):  
TING MU ◽  
DACHENG FENG ◽  
SHENGYU FENG
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulations ◽  
Silicon Atom ◽  
Minimum Energy ◽  
Core Structure ◽  
The Core ◽  
Molecular Modeling Study ◽  
Dynamics Simulations ◽  
Energy Configurations

This paper focuses on the maximum generation issue. Molecular dynamics simulations have been employed to search the minimum energy configurations of eight types of structurally related polysilane dendrimers of various generations. Calculations reveal that for the studied dendrimers, the innermost Si – Si bonds adjoining the silicon atom at the center of the core structure are extended for steric relief with the amount of extension increasing with the number of generations due to the rise of the spatial hindrance inside these molecules.

scholarly journals Homology modeling and molecular dynamics simulations of MUC1-9/H-2Kb complex suggest novel binding interactions

2010 ◽  
Vol 17 (7) ◽  
pp. 1817-1829 ◽  
Author(s):  
Athanassios Stavrakoudis ◽  
Ioannis G. Tsoulos ◽  
Katalin Uray ◽  
Ferenc Hudecz ◽  
Vasso Apostolopoulos
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Binding Interactions ◽  
Dynamics Simulations

scholarly journals Adsorption on Ligand-Tethered Nanoparticles

2021 ◽  
Vol 22 (16) ◽  
pp. 8810
Author(s):  
Małgorzata Borówko ◽  
Tomasz Staszewski
Keyword(s):  
Molecular Dynamics ◽  
Adsorption Isotherm ◽  
Molecular Dynamics Simulations ◽  
Polymer Coatings ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Structural Transitions ◽  
Excess Adsorption ◽  
The Core ◽  
Dynamics Simulations

We use coarse-grained molecular dynamics simulations to study adsorption on ligand-tethered particles. Nanoparticles with attached flexible and stiff ligands are considered. We discuss how the excess adsorption isotherm, the thickness of the polymer corona, and its morphology depend on the number of ligands, their length, the size of the core, and the interaction parameters. We investigate the adsorption-induced structural transitions of polymer coatings. The behavior of systems involving curved and flat “brushes” is compared.

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