Molecular modeling and molecular dynamics simulation studies on thyroid hormone receptor from Rattus norvegicus: role of conserved water molecules

Journal of Molecular Modeling ◽

10.1007/s00894-021-04740-1 ◽

2021 ◽

Vol 27 (5) ◽

Author(s):

Soumita Mukherjee ◽

Subrata Dasgupta ◽

Utpal Adhikari ◽

Sujit Sankar Panja

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Rattus Norvegicus ◽

Thyroid Hormone Receptor ◽

Dynamics Simulation ◽

Water Molecules ◽

Simulation Studies ◽

Conserved Water Molecules

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Identification of natural compound inhibitors against Pf DXR: A hybrid structure‐based molecular modeling approach and molecular dynamics simulation studies

Journal of Cellular Biochemistry ◽

10.1002/jcb.28714 ◽

2019 ◽

Vol 120 (9) ◽

pp. 14531-14543 ◽

Author(s):

Anu Manhas ◽

Dhaval Patel ◽

Mohsin Y. Lone ◽

Prakash C. Jha

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Natural Compound ◽

Hybrid Structure ◽

Dynamics Simulation ◽

Simulation Studies ◽

Modeling Approach

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Exploration of the selective binding mechanism of GSK3β via molecular modeling and molecular dynamics simulation studies

Medicinal Chemistry Research ◽

10.1007/s00044-020-02514-7 ◽

2020 ◽

Vol 29 (4) ◽

pp. 690-698

Author(s):

Linkai Mou ◽

Zilong Ma ◽

Xiaomin Meng ◽

Wenxing Li ◽

Shuai Liang ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Studies ◽

Binding Mechanism ◽

Selective Binding

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Molecular Modeling and Molecular Dynamics Simulation Studies on the Interactions of Hydroxylated Polychlorinated Biphenyls with Estrogen Receptor-β

Archives of Environmental Contamination and Toxicology ◽

10.1007/s00244-013-9916-2 ◽

2013 ◽

Vol 65 (3) ◽

pp. 357-367 ◽

Author(s):

Xiaolin Li ◽

Li Ye ◽

Xiaoxiang Wang ◽

Wei Shi ◽

XiangPing Qian ◽

...

Keyword(s):

Molecular Dynamics ◽

Estrogen Receptor ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Polychlorinated Biphenyls ◽

Estrogen Receptor Β ◽

Dynamics Simulation ◽

Simulation Studies ◽

Hydroxylated Polychlorinated Biphenyls

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Role of hydrophilic and hydrophobic contacts in folding of the second ?-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10065 ◽

2002 ◽

Vol 47 (2) ◽

pp. 154-162 ◽

Author(s):

Yaoqi Zhou ◽

Apichart Linhananta

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Protein G ◽

Simulation Studies ◽

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Role of Dynamic Heterogeneities in Ionic Liquids: Insights from All-Atom and Coarse-Grained Molecular Dynamics Simulation Studies

ChemPhysChem ◽

10.1002/cphc.201700504 ◽

2017 ◽

Vol 18 (16) ◽

pp. 2233-2242 ◽

Author(s):

Tamisra Pal ◽

Michael Vogel

Keyword(s):

Molecular Dynamics ◽

Ionic Liquids ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Coarse Grained ◽

Simulation Studies ◽

Coarse Grained Molecular Dynamics

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Theoretical investigation on the glycan-binding specificity ofAgrocybe cylindraceagalectin using molecular modeling and molecular dynamics simulation studies

Journal of Molecular Recognition ◽

10.1002/jmr.2468 ◽

2015 ◽

Vol 28 (9) ◽

pp. 528-538 ◽

Author(s):

Ponnusamy Parasuraman ◽

Veeramani Murugan ◽

Jeyasigamani F A Selvin ◽

M Michael Gromiha ◽

Kazuhiko Fukui ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Theoretical Investigation ◽

Binding Specificity ◽

Dynamics Simulation ◽

Simulation Studies

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Molecular Modeling and Molecular Dynamics Simulation Studies of the GSK3β/ATP/Substrate Complex: Understanding the Unique P+4 Primed Phosphorylation Specificity for GSK3β Substrates

Journal of Chemical Information and Modeling ◽

10.1021/ci100493j ◽

2011 ◽

Vol 51 (5) ◽

pp. 1025-1036 ◽

Author(s):

Shao-Yong Lu ◽

Yong-Jun Jiang ◽

Jian-Wei Zou ◽

Tian-Xing Wu

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Studies ◽

Substrate Complex

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Role of invariant water molecules in retaining the active site geometry of β-lactamase: a molecular dynamics simulation study

Molecular Simulation ◽

10.1080/08927022.2011.590984 ◽

2011 ◽

Vol 37 (15) ◽

pp. 1234-1238 ◽

Author(s):

K. V. Dileep ◽

I. Tintu ◽

N. V. Vinod ◽

P. P. Saliha ◽

C. Sadasivan

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Active Site ◽

Dynamics Simulation ◽

Water Molecules

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Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex

Journal of Biomolecular Structure and Dynamics ◽

10.1080/073911011010524996 ◽

2011 ◽

Vol 29 (3) ◽

pp. 595-595

Author(s):

R. Majumder ◽

S. Roy ◽

A. R. Thakur

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Studies

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Understanding the regulation mechanisms of PAF receptor by agonists and antagonists: Molecular modeling and molecular dynamics simulation studies

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21213 ◽

2007 ◽

Vol 67 (1) ◽

pp. 41-52 ◽

Author(s):

Chunshan Gui ◽

Weiliang Zhu ◽

Gang Chen ◽

Xiaomin Luo ◽

Oi W. Liew ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Studies ◽

Regulation Mechanisms ◽

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