The Mg2+ Binding Sites of the 5S rRNA Loop E Motif as Investigated by Molecular Dynamics Simulations

Binding Sites ◽

5S Rrna ◽

Symmetric K+ and Mg2+ Ion-binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations

Journal of Molecular Biology ◽

10.1016/j.jmb.2003.10.057 ◽

2004 ◽

Vol 335 (2) ◽

pp. 555-571 ◽

Cited By ~ 58

Author(s):

Pascal Auffinger ◽

Lukasz Bielecki ◽

Eric Westhof

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

5S Rrna ◽

Ion Binding ◽

Ion Binding Sites ◽

Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.0c01420 ◽

2021 ◽

Author(s):

Guoqin Feng ◽

Xiangying Zhang ◽

Yan Li ◽

Renxiao Wang

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

Molecular Dynamics Simulations Suggest Multiple Binding Sites for Phospholamban on SERCA

Biophysical Journal ◽

10.1016/j.bpj.2016.11.3070 ◽

2017 ◽

Vol 112 (3) ◽

pp. 570a

Author(s):

Nikolai Smolin ◽

Vidhya Sivakumaran ◽

Seth L. Robia

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

Multiple Binding Sites ◽

Multiple Binding ◽

Molecular Dynamics Simulations of Kir2.2 and Cholesterol Reveal State- and Concentration-Dependent Binding Sites

Biophysical Journal ◽

10.1016/j.bpj.2018.11.266 ◽

2019 ◽

Vol 116 (3) ◽

pp. 41a

Author(s):

Nicolas Barbera ◽

Manuela A. Ayee ◽

Belinda S. Akpa ◽

Irena Levitan

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

Accounts of Chemical Research ◽

10.1021/acs.accounts.9b00613 ◽

2020 ◽

Vol 53 (3) ◽

pp. 654-661 ◽

Cited By ~ 7

Author(s):

Antonija Kuzmanic ◽

Gregory R. Bowman ◽

Jordi Juarez-Jimenez ◽

Julien Michel ◽

Francesco L. Gervasio

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

Cryptic Binding Sites ◽

Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations

The Journal of Physical Chemistry Letters ◽

10.1021/acs.jpclett.0c03182 ◽

2020 ◽

pp. 65-72

Author(s):

Matteo Carli ◽

Giulia Sormani ◽

Alex Rodriguez ◽

Alessandro Laio

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

Large Scale ◽

Allosteric Inhibition ◽

Main Protease ◽

Distribution and favorable binding sites of pyrroloquinoline and its analogues in a lipid bilayer studied by molecular dynamics simulations

Biophysical Chemistry ◽

10.1016/j.bpc.2008.05.006 ◽

2008 ◽

Vol 136 (2-3) ◽

pp. 128-135 ◽

Cited By ~ 17

Author(s):

Alexander Kyrychenko ◽

Jacek Waluk

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayer ◽

Binding Sites ◽

Molecular dynamics simulations of Zn2+ coordination in protein binding sites

The Journal of Chemical Physics ◽

10.1063/1.3428381 ◽

2010 ◽

Vol 132 (20) ◽

pp. 205101 ◽

Cited By ~ 11

Author(s):

Richard Tjörnhammar ◽

Olle Edholm

Keyword(s):

Molecular Dynamics ◽

Protein Binding ◽

Binding Sites ◽

Protein Binding Sites ◽

Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations

The Journal of Physical Chemistry Letters ◽

10.1021/jz2011379 ◽

2011 ◽

Vol 2 (19) ◽

pp. 2504-2508 ◽

Cited By ~ 48

Author(s):

Vincenzo Carnevale ◽

Werner Treptow ◽

Michael L. Klein

Keyword(s):

Molecular Dynamics ◽

Ion Channel ◽

Binding Sites ◽

Sodium Ion ◽

Ion Binding ◽

Ion Binding Sites ◽

Accurate Detection of Protein:Ligand Binding Sites Using Molecular Dynamics Simulations

Structure ◽

10.1016/j.str.2004.09.005 ◽

2004 ◽

Vol 12 (11) ◽

pp. 1989-1999 ◽

Cited By ~ 16

Author(s):

Akshay Bhinge ◽

Purbani Chakrabarti ◽

Kavitha Uthanumallian ◽

Kanika Bajaj ◽

Kausik Chakraborty ◽

...

Keyword(s):

Molecular Dynamics ◽

Binding Sites ◽

Accurate Detection ◽