Use of a potential of mean force to analyze free energy contributions in protein folding

Biochemistry ◽  
1992 ◽  
Vol 31 (27) ◽  
pp. 6290-6297 ◽  
Author(s):  
F. Avbelj
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Potential Of Mean Force

scholarly journals Advances in free-energy-based simulations of protein folding and ligand binding

2016 ◽  
Vol 36 ◽  
pp. 25-31 ◽  
Author(s):  
Alberto Perez ◽  
Joseph A Morrone ◽  
Carlos Simmerling ◽  
Ken A Dill
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Ligand Binding

scholarly journals Calculating free energies of organic molecules on insulating substrates

2017 ◽  
Vol 8 ◽  
pp. 667-674
Author(s):  
Julian Gaberle ◽  
David Z Gao ◽  
Alexander L Shluger
Keyword(s):  
Free Energy ◽  
Organic Molecules ◽  
Computational Cost ◽  
Potential Of Mean Force ◽  
Free Energies ◽  
Energy Profiles ◽  
Integration Techniques ◽  
Ring Structures ◽  
Anchoring Groups ◽  
Insulating Substrates

The challenges and limitations in calculating free energies and entropies of adsorption and interaction of organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free energy profiles and entropy changes were calculated for step adhesion and dimer formation of these molecules. However, converging these calculations is nontrivial and comes at large computational cost. We illustrate the difficulties as well as the possibilities of applying these methods towards understanding dynamic processes of organic molecules on insulating substrates.

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