scholarly journals Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: Catalytic efficiency regulated by substrate binding

2004 ◽  
Vol 57 (4) ◽  
pp. 747-757 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cysteine Proteinase ◽  
Substrate Binding ◽  
Three Dimensional ◽  
Catalytic Efficiency ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Dynamics Simulations

Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA

Biochemistry ◽  
1990 ◽  
Vol 29 (45) ◽  
pp. 10317-10322 ◽  
Author(s):  
Lennart Nilsson ◽  
Agneta Aahgren-Staalhandske ◽  
Ann Sofie Sjoegren ◽  
Solveig Hahne ◽  
Britt Marie Sjoeberg
Keyword(s):  
Molecular Dynamics ◽  
Active Site ◽  
Messenger Rna ◽  
Bacteriophage T4 ◽  
Three Dimensional ◽  
The Self ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Self Splicing

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1

2018 ◽  
Vol 20 (9) ◽  
pp. 6409-6420 ◽  
Author(s):  
Juan Duan ◽  
Chuncai Hu ◽  
Jiafan Guo ◽  
Lianxian Guo ◽  
Jia Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
New Delhi ◽  
Binding Process ◽  
Dynamics Simulations

We have investigated the substrate-binding pathways of NDM-1 via unbiased molecular dynamics simulations and metadynamics.

Molecular Dynamics Simulations As a Tool to Investigate the Three-Dimensional Diversity of Peptide and Pseudopeptide Libraries

2007 ◽  
pp. 209-221 ◽  
Author(s):  
Gérard Grassy ◽  
Abdelaziz Yasri ◽  
Pierre Sans ◽  
Anne-Marie Armbruster ◽  
Roger Lahana ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Dynamics Simulations

Molecular-Dynamics Simulations of Granular Axial Segregation in a Rotating Cylinder

1998 ◽  
Vol 12 (04) ◽  
pp. 115-122 ◽  
Author(s):  
Sakamoto Shoichi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Process ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Rotating Cylinder ◽  
Axial Segregation ◽  
Cohesive Forces ◽  
Dynamics Simulations ◽  
Different Diameters ◽  
Narrow Bands

In order to investigate segregation of granular binary-mixtures in a horizontally rotating cylinder, three-dimensional molecular dynamics simulations are carried out. Two kinds of particles, which have different diameters and/or different roughness of surfaces, are segregated into three bands. It is found that particles receive averaged force cohesively at the boundaries of segregated bands. The present analysis shows that segregated narrow bands are formed by diffusion process and that the cohesive forces operating at the boundaries stabilize them.

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