Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy

2007 ◽  
Vol 4 (1) ◽  
pp. 192-208 ◽  
Author(s):  
Srinath Cheluvaraja ◽  
Hagai Meirovitch
Keyword(s):  
Free Energy ◽  
Absolute Entropy ◽  
The Absolute

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.

Zeros of a complex Ginzburg–Landau order parameter with applications to superconductivity

1994 ◽  
Vol 5 (4) ◽  
pp. 431-448 ◽  
Author(s):  
C. M. Elliott ◽  
H. Matano ◽  
Tang Qi
Keyword(s):  
Free Energy ◽  
Numerical Simulations ◽  
Gibbs Free Energy ◽  
Order Parameter ◽  
Magnetic Potential ◽  
Ginzburg Landau ◽  
Absolute Value ◽  
Complex Order ◽  
Isolated Points ◽  
The Absolute

We consider the minimizers of the Gibbs free energy which couples a complex Ginzburg–Landau order parameter with a magnetic potential. It is established that the set on which the complex order parameter equals zero consists only of isolated points. Some estimates concerning the set on which the absolute value of the order parameter is small are also given. Numerical simulations are presented for the problem without a magnetic potential.

scholarly journals Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 686 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
David L. Mobley
Keyword(s):  
Free Energy ◽  
Chemical Potential ◽  
Computational Cost ◽  
Energy Model ◽  
Free Energy Calculations ◽  
Limiting Factor ◽  
Solubility Prediction ◽  
Energy Calculations ◽  
Chemical Potentials ◽  
The Absolute

Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations.  We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation.    Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use.

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