Engineering Strontium Binding Affinity in an EF-hand Motif: A Quantum Chemical and Molecular Dynamics Study

2004 ◽  
Vol 22 (3) ◽  
pp. 281-297 ◽  
Author(s):  
David Rinaldo ◽  
Claudio Vita ◽  
Martin J. Field
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Quantum Chemical ◽  
Ef Hand

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

scholarly journals Modulating Uranium Binding Affinity in Engineered Calmodulin EF-Hand Peptides: Effect of Phosphorylation

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e41922 ◽  
Author(s):  
Romain Pardoux ◽  
Sandrine Sauge-Merle ◽  
David Lemaire ◽  
Pascale Delangle ◽  
Luc Guilloreau ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Ef Hand

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

Investigation of the interfacial behavior of organics on sulfide semiconductor surfaces by quantum chemical calculations and molecular dynamics simulations

2021 ◽  
Author(s):  
Haiding Zhu ◽  
Xuefeng Ren ◽  
Shengxiang Yan ◽  
Xingyou Liang ◽  
Liguo Gao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical Calculations ◽  
Organic Pollutants ◽  
Quantum Chemical ◽  
Semiconductor Surfaces ◽  
Interfacial Behavior ◽  
The World ◽  
Dynamics Simulations

The presence of organic pollutants in the world is harmful to our existence and the environment.

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