Molecular dynamics insights into the structure, function, and substrate binding mechanism of mucin desulfating sulfatase of gut microbe
            Bacteroides fragilis

Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins

BMC Bioinformatics ◽

10.1186/s12859-018-2348-2 ◽

2018 ◽

Vol 19 (1) ◽

Author(s):

Nicolás Stocchi ◽

María Victoria Revuelta ◽

Priscila Ailín Lanza Castronuovo ◽

D. Mariano A. Vera ◽

Arjen ten Have

Keyword(s):

Molecular Dynamics ◽

Structure Function ◽

Function Analysis ◽

Substrate Binding ◽

Functional Diversification

Investigating the substrate binding mechanism of sulfotransferase 2A1 based on substrate tunnel analysis: a molecular dynamics simulation study

Journal of Molecular Modeling ◽

10.1007/s00894-016-3041-x ◽

2016 ◽

Vol 22 (8) ◽

Author(s):

Li Zhao ◽

Pupu Zhang ◽

Shiyang Long ◽

Linlin Wang ◽

Hanyong Jin ◽

...

Keyword(s):

Molecular Dynamics ◽

Simulation Study ◽

Substrate Binding ◽

Dynamics Simulation ◽

Binding Mechanism ◽

Tunnel Analysis

Molecular insights into substrate binding mechanism of undecaprenyl pyrophosphate with membrane integrated phosphatidyl glycerophosphate phosphatase B (PgpB) using molecular dynamics simulation approach

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1449666 ◽

2018 ◽

Vol 37 (4) ◽

pp. 1062-1089 ◽

Cited By ~ 2

Author(s):

Manish Kesherwani ◽

Devadasan Velmurugan

Keyword(s):

Molecular Dynamics ◽

Substrate Binding ◽

Dynamics Simulation ◽

Simulation Approach ◽

Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

Biochemistry ◽

10.1021/bi5015612 ◽

2015 ◽

Vol 54 (9) ◽

pp. 1841-1848 ◽

Cited By ~ 17

Author(s):

Qi Chen ◽

Zheng-Jiao Luan ◽

Xiaolin Cheng ◽

Jian-He Xu

Keyword(s):

Molecular Dynamics ◽

Substrate Binding ◽

1P006 Molecular dynamics simulation of 3α-hydroxysteroid dehydrogenase with NADH : Structural changes in the substrate-binding loop(Proteins-structure and structure-function relationship,Oral Presentations)

Seibutsu Butsuri ◽

10.2142/biophys.47.s25_1 ◽

2007 ◽

Vol 47 (supplement) ◽

pp. S25

Author(s):

Shota Nakamura ◽

Tomotaka Oroguchi ◽

Tsutomu Yamane ◽

Mitsunori Ikeguchi ◽

Sachiyo Kataoka ◽

...

Keyword(s):

Molecular Dynamics ◽

Structure Function ◽

Structural Changes ◽

Substrate Binding ◽

Hydroxysteroid Dehydrogenase ◽

Dynamics Simulation ◽

Function Relationship ◽

Oral Presentations ◽

Binding Loop

Faculty Opinions recommendation of Analysis of activator-binding sites on the APC/C supports a cooperative substrate-binding mechanism.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1159981.619666 ◽

2009 ◽

Author(s):

Jane Endicott

Keyword(s):

Binding Sites ◽

Substrate Binding ◽

Binding mechanism of naringenin with monoamine oxidase – B enzyme: QM/MM and molecular dynamics perspective

Heliyon ◽

10.1016/j.heliyon.2021.e06684 ◽

2021 ◽

Vol 7 (4) ◽

pp. e06684

Author(s):

Hunday Govindasamy ◽

Sivanandam Magudeeswaran ◽

Saravanan Kandasamy ◽

Kumaradhas Poomani

Keyword(s):

Molecular Dynamics ◽

Monoamine Oxidase ◽

Monoamine Oxidase B ◽

Investigation on the Interaction of Dabrafenib with Human Serum Albumin Using Combined Experiment and Molecular Dynamics Simulation: Exploring the Binding Mechanism, Esterase-like Activity, and Antioxidant Activity

Molecular Pharmaceutics ◽

10.1021/acs.molpharmaceut.8b00806 ◽

2018 ◽

Vol 15 (12) ◽

pp. 5637-5645 ◽

Cited By ~ 2

Author(s):

Zili Suo ◽

Xinnuo Xiong ◽

Qiaomei Sun ◽

Ludan Zhao ◽

Peixiao Tang ◽

...

Keyword(s):

Molecular Dynamics ◽

Antioxidant Activity ◽

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Dynamics Simulation ◽

2P010 Molecular dynamics simulation of the terminal oxygenase component of carbazole 1,9a-dioxygenase(Proteins-structure and structure-function relationship,Poster Presentations)

Seibutsu Butsuri ◽

10.2142/biophys.47.s115_3 ◽

2007 ◽

Vol 47 (supplement) ◽

pp. S115

Author(s):

Yu Inoue ◽

Tohru Terada ◽

Shugo Nakamura ◽

Kentaro Shimizu

Keyword(s):

Molecular Dynamics ◽

Structure Function ◽

Dynamics Simulation ◽

Structure Function Relationship ◽

Function Relationship ◽

Poster Presentations

1P003 Molecular dynamics simulations of the ligand-binding core of the inositol 1,4,5-trisphosphate receptor in the ligand-free slate(Proteins-structure and structure-function relationship,Oral Presentations)

Seibutsu Butsuri ◽

10.2142/biophys.47.s24_2 ◽

2007 ◽

Vol 47 (supplement) ◽

pp. S24

Author(s):

Yoichi Ida ◽

Sotaro Fuchigami ◽

Mitsunori Ikeguchi ◽

Akinori Kidera

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Structure Function ◽

Ligand Free ◽

Inositol 1,4,5 Trisphosphate ◽

Binding Core ◽

Function Relationship ◽

Dynamics Simulations ◽

Trisphosphate Receptor ◽

Oral Presentations