Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations

2018 ◽  
Vol 20 (14) ◽  
pp. 9101-9107 ◽  
Author(s):  
Daniel Bonhenry ◽  
François Dehez ◽  
Mounir Tarek
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Free Energy ◽  
Lipid Bilayers ◽  
Free Energy Calculations ◽  
Phospholipid Bilayer ◽  
Protonation State ◽  
Energy Calculations ◽  
Energy Surfaces

Protonation states of amino acids crossing lipid bilayers from multidimensional free energy surfaces.

scholarly journals Insight into the Binding of DFG-out Allosteric Inhibitors to B-Raf Kinase Using Molecular Dynamics and Free Energy Calculations

2015 ◽  
Vol 11 (2) ◽  
pp. 124-136 ◽  
Author(s):  
Luis Coronel ◽  
Jose Granadino-Roldán ◽  
Marta Pinto ◽  
Maria Tomas ◽  
Maria Pujol ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Allosteric Inhibitors ◽  
Energy Calculations ◽  
Raf Kinase ◽  
Insight Into

Small-to-Large Length Scale Transition of TMAO Interaction with Hydrophobic Solutes

2021 ◽  
Author(s):  
Angelina Folberth ◽  
Swaminath Bharadwaj ◽  
Nico van der Vegt
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Length Scale ◽  
Simulation Data ◽  
Energy Calculations ◽  
Large Length ◽  
Hydrophobic Solutes ◽  
Large Length Scale

We report the effect of trimethylamine N-oxide (TMAO) on the solvation of nonpolar solutes in water studied with molecular dynamics (MD) simulations and free-energy calculations. The simulation data indicate the...

scholarly journals Accurate calculation of the absolute free energy of binding for drug molecules

2016 ◽  
Vol 7 (1) ◽  
pp. 207-218 ◽  
Author(s):  
Matteo Aldeghi ◽  
Alexander Heifetz ◽  
Michael J. Bodkin ◽  
Stefan Knapp ◽  
Philip C. Biggin
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Accurate Calculation ◽  
Energy Calculations ◽  
Thermodynamic Cycles ◽  
Drug Molecules ◽  
The Absolute ◽  
Free Energy Of Binding

Free energy calculations based on molecular dynamics and thermodynamic cycles accurately reproduce experimental affinities of diverse bromodomain inhibitors.

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