We have developed a method for calculating the stability in water of protein structures, starting from their atomic coordinates. The contribution of each protein atom to the solvation free energy is estimated as the product of the accessibility of the atom to solvent and its atomic solvation parameter. Applications of the method include estimates of the relative stability of different protein conformations, estimates of the free energy of binding of ligands to proteins and atomic-level descriptions of hydrophobicity and amphiphilicity.