Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis

Energy Analysis ◽

Binding Free Energy ◽

Rational Drug Design ◽

Dynamics Simulation ◽

Rational Drug ◽

Combined Strategy ◽

Employing the combined strategy to identify novel CCR5 inhibitors and provide a basis for rational drug design.

Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor‐α through molecular dynamics simulation and binding free energy analysis

Journal of Computational Chemistry ◽

10.1002/jcc.26076 ◽

2019 ◽

Vol 41 (2) ◽

pp. 97-109 ◽

Cited By ~ 1

Author(s):

Kalaiarasi Chinnasamy ◽

Manjula Saravanan ◽

Kumaradhas Poomani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Estrogen Receptor ◽

Energy Analysis ◽

Binding Free Energy ◽

Estrogen Receptor Α ◽

Dynamics Simulation ◽

Binding Mechanism ◽

Binding mechanism, conformation, and stability of diflunisal and mycophenolic acid with p300 HAT enzyme using molecular dynamics simulation and binding free energy analysis

Medicinal Chemistry Research ◽

10.1007/s00044-020-02500-z ◽

2020 ◽

Vol 29 (3) ◽

pp. 504-518

Author(s):

Sivanandam Magudeeswaran ◽

Kumaradhas Poomani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Mycophenolic Acid ◽

Energy Analysis ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Binding Mechanism ◽

The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis

Journal of Molecular Modeling ◽

10.1007/s00894-016-2907-2 ◽

2016 ◽

Vol 22 (2) ◽

Cited By ~ 4

Author(s):

Xiaoping Quan ◽

Xiuqiang Chen ◽

Deliang Sun ◽

Bo Xu ◽

Linlin Zhao ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Simulation Study ◽

Energy Analysis ◽

Dynamics Simulation ◽

Insight into mechanism of small molecule inhibitors of the MDM2–p53 interaction: Molecular dynamics simulation and free energy analysis

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2011.06.003 ◽

2011 ◽

Vol 30 ◽

pp. 46-53 ◽

Cited By ~ 28

Author(s):

Jianzhong Chen ◽

Jinan Wang ◽

Beisi Xu ◽

Weiliang Zhu ◽

Guohui Li

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Small Molecule ◽

Energy Analysis ◽

Small Molecule Inhibitors ◽

Dynamics Simulation ◽

Free Energy Analysis ◽

Insight Into

Molecular Mechanism of MDM2 with Novel Small Inhibitor Recognition Explored by Molecular Dynamics Simulation and Free Energy Analysis

Asian Journal of Chemistry ◽

10.14233/ajchem.2015.17382 ◽

2015 ◽

Vol 27 (5) ◽

pp. 1589-1592

Author(s):

Hui Li ◽

Shi-Kui Hu ◽

Xu Wen ◽

Xi-Hai Liang ◽

Hong Zeng

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Mechanism ◽

Energy Analysis ◽

Dynamics Simulation ◽

Free Energy Analysis ◽

Inhibitor Recognition

Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b08241 ◽

2018 ◽

Vol 122 (13) ◽

pp. 3219-3229 ◽

Cited By ~ 11

Author(s):

Tomoko Mizuguchi ◽

Nobuyuki Matubayasi

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Analysis ◽

Lipid Membrane ◽

Peptide Binding ◽

Dynamics Simulation ◽

Free-energy analysis of lysozyme–triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

Chemical Physics Letters ◽

10.1016/j.cplett.2012.12.063 ◽

2013 ◽

Vol 559 ◽

pp. 94-98 ◽

Cited By ~ 7

Author(s):

Kazuhiro Takemura ◽

Raghunadha Reddy Burri ◽

Takeshi Ishikawa ◽

Takakazu Ishikura ◽

Shun Sakuraba ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Analysis ◽

Dynamics Simulation ◽

Binding Modes ◽

Solution Theory ◽

Molecular Dynamics Simulation of Tryptophan Hydroxylase-1: Binding Modes and Free Energy Analysis to Phenylalanine Derivative Inhibitors

International Journal of Molecular Sciences ◽

10.3390/ijms14059947 ◽

2013 ◽

Vol 14 (5) ◽

pp. 9947-9962 ◽

Cited By ~ 22

Author(s):

Hao Zhong ◽

Wei Huang ◽

Gu He ◽

Cheng Peng ◽

Fengbo Wu ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Analysis ◽

Tryptophan Hydroxylase ◽

Dynamics Simulation ◽

Binding Modes ◽

Influence of Hyperthermophilic Protein Cren7 on the Stability and Conformation of DNA: Insights from Molecular Dynamics Simulation and Free Energy Analysis

The Journal of Physical Chemistry B ◽

10.1021/jp305860h ◽

2012 ◽

Vol 116 (41) ◽

pp. 12415-12425 ◽

Cited By ~ 18

Author(s):

Lin Chen ◽

Ji-Long Zhang ◽

Li-Ying Yu ◽

Qing-Chuan Zheng ◽

Wen-Ting Chu ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Analysis ◽

Dynamics Simulation ◽

The Stability ◽

Free Energy Analysis ◽

Hyperthermophilic Protein

Recognition mechanism of Wilms’ tumour suppressor protein and DNA triplets: insights from molecular dynamics simulation and free energy analysis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1433066 ◽

2018 ◽

Vol 37 (3) ◽

pp. 562-575 ◽

Cited By ~ 1

Author(s):

Ling-Fei Zhang ◽

Qing-Chuan Zheng ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Analysis ◽

Tumour Suppressor ◽

Dynamics Simulation ◽

Wilms Tumour ◽

Recognition Mechanism ◽

Tumour Suppressor Protein ◽