Protein surrounding Water Visualization and Energetics
Solvation Free Energy
Solvation free energy of a protein is the Gibbs free energy change associated with the solvation
process, i.e., transferring a protein from a vacuum phase (an isolated protein) to a solution phase (a
protein surrounded by waters and ions). Solvation free energy thus quantifies the strength and nature of
the protein-solvent interactions, and is the fundamental thermodynamic quantity dictating the
conformational stability of proteins, protein-ligand binding affinity, and protein-protein interactions.
It is also a key parameter to understand protein aggregation that is linked to diverse human diseases.
This server provides an automated and user-friendly interface for obtaining the solvation free energy of
a protein, which is computed based on the molecular theory of solvation. Users only need to upload a PDB
file of a protein of interest. One of the highlights of our server is that it offers the site-directed
thermodynamic analysis developed in our lab, i.e., the decomposition of the protein solvation free
energy into contributions from constituent amino acids, which is valuable for identifying thermodynamic
hot spots. We will also soon support accepting multiple PDF files so that users can analyze changes in
thermodynamic quantities that occur during protein conformational dynamics of interest (fluctuating
thermodynamics analysis). Our server will keep evolving to provide better user-interface and more
accurate solvation free energy. Please enjoy this PROWAVE server and let us know how you think.