Secondary structure bias in generalized born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

Article Abstract:

A comparative study of the conformational ensembles and free energies of solvent polarization from explicit, as well as an implicit solvation is used to analyze the secondary structure bias in the generalized born (GB) solvent models. Despite the fact that GB models can be implemented only by optimizing the effective Born radius calculations, analysis has proved to be extremely beneficial, as the GB function proves the agreement between the self and interaction energies.

Usage, Thermal properties, Alanine, Report

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Solvation free energies and transfer free energies for Amino acids from hydrophobic solution to water solution from a very simple residue model

Article Abstract:

A study was conducted, using molecular dynamics simulations and thermodynamic integration, to investigate the solvation free energy changes for transferring the 20 amino acids, in their neutral state from hydrophobic solution to aqueous solution. The result indicates that the entropic contribution to the free energy is very important and cannot be neglected.

Gibbs' free energy

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Are solvation free energies of homogenous helical peptides additive?

Article Abstract:

The additivity of the solvation free energy of amino acids in homogenous helices of different length in water and in chloroform is investigated. The investigation focused on homogenous peptides composed of uncharged amino acids, where the backbone atoms are kept fixed in an ideal helical conformation.

Peptides, Atomic properties

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