All Questions
Tagged with free-energy proteins
5
questions
2
votes
2
answers
242
views
Loss of entropy and solvation energy in proteins
I am reading a chapter on protein stability. One section outlines the role of salt bridges or ion pairs in the stability of a protein. The excerpt goes as follows (italization added for emphasis):
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- 265
6
votes
1
answer
206
views
Biomolecular energy functions and entropy
From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
- 163
1
vote
1
answer
439
views
How can absolute binding free energies be calculated?
In the calculation of binding free energies, such as between a protein and a ligand, I learned that absolute values cannot be obtained from simulation (such as taught in this lecture, slide 2). Rather,...
- 1,118
2
votes
0
answers
529
views
NAMD free energy calculations (FEP, Alchemical)
I am trying to calculate the absolute free energy of a protein-ligand-complex using the free energy perturbation theory.
Following the alchemical route in this tutorial, I have calculated eight MD-...
- 661
1
vote
0
answers
208
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Energy required to break salt bridges in peptides and proteins
Is there a way to calculate the energy required to break a salt bridge in a peptide or on the exposed surface of a protein in aqueous solution? Is there any useful literature on this topic? I'm ...
- 11