Surrounding water


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.