Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

2009 ◽  
Vol 392 (5) ◽  
pp. 1339-1356 ◽  
Author(s):  
Martin Klvana ◽  
Martina Pavlova ◽  
Tana Koudelakova ◽  
Radka Chaloupkova ◽  
Pavel Dvorak ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Product Release ◽  
Random Acceleration ◽  
Dynamics Simulations ◽  
Random Acceleration Molecular Dynamics

scholarly journals Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels

RSC Advances ◽  
2020 ◽  
Vol 10 (72) ◽  
pp. 43994-44002
Author(s):  
Yue Pan ◽  
Renrui Qi ◽  
Minghao Li ◽  
Bingda Wang ◽  
Honglan Huang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Adenosine Deaminase ◽  
Closed Conformation ◽  
Open Conformation ◽  
Nucleoside Metabolism ◽  
Critical Residues ◽  
Random Acceleration ◽  
Dynamics Simulations ◽  
Important Enzyme

Adenosine deaminase (ADA), an important enzyme related to purine nucleoside metabolism, can be divided into open conformation and closed conformation according to the inhibitors of binding.

Exploring the different ligand escape pathways in acylaminoacyl peptidase by random acceleration and steered molecular dynamics simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (13) ◽  
pp. 10987-10996 ◽  
Author(s):  
Hanyong Jin ◽  
Jingxuan Zhu ◽  
Yang Dong ◽  
Weiwei Han
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Steered Molecular Dynamics ◽  
Prolyl Oligopeptidase ◽  
Acylaminoacyl Peptidase ◽  
Random Acceleration ◽  
Dynamics Simulations

Acylaminoacyl peptidase (APH, EC 3.4.19.1) is a novel class of serine-type protease belonging to the prolyl oligopeptidase (POP) family.

Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations

2016 ◽  
Vol 18 (7) ◽  
pp. 5622-5629 ◽  
Author(s):  
Yuzhen Niu ◽  
Shuyan Li ◽  
Dabo Pan ◽  
Huanxiang Liu ◽  
Xiaojun Yao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Residence Time ◽  
Computational Study ◽  
Steered Molecular Dynamics ◽  
The Difference ◽  
Random Acceleration ◽  
Dynamics Simulations

Random acceleration and steered molecular dynamics simulations reveal the unbinding pathway of B-RAF inhibitors and the difference in the residence time.

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