The retention of proteins in hydrophobic interaction chromatographic (HIC) systems was investigated using the preferential interaction theory in concert with quantitative structure property relationship (QSPR) modeling. The numbers of water molecules and salt ions released upon protein binding were determined from In (k') vs. salt concentration plots for a large number of proteins with a range of properties. The effect of salt type on protein binding was also studied by comparing the number of water molecules released in the presence of different salts. Quantitative structure property relationship (QSPR) models based on a support vector machine (SVM) approach were successfully generated for predicting the water molecules released values. These models employed protein crystal structure and primary sequence information as well as a set of hydrophobicity descriptors based on the solvent accessible surface area of the proteins. In addition to successfully predicting the water release values, the selected descriptors provide insights into the protein physicochemical properties which influence protein affinity in HIC system. (c) 2007 Elsevier Ltd. All rights reserved.