Parker Method for Prediction of surface sites
Parker et al. has produced following hydrophilicity scale derived from High-Performance Liquid Chromatography (HPLC) Peptide Retention Data. Surface Profile: The surface profile for a protein was determined by summing the parameters for each residue of seven-residue segment and assigning this sum to the fourth residue. This procedure was repeated by shifting the segment by one residue from the N-to the C-terminus. A plot of these values against the residue number using either HPLC, accessiblity, bulk hydrophobic character, hydrophobicity, global, pi, or hydropathy parameters (Here only HPLC is used) provided a surface profile. To objectively interpret all of these profiles, Parker et al. has used following arbitary of rules: 1) The average surface hydrophilicity is defined as the the mean of the profile values for a protein using a particular parameter set. 2) Any residue with a profile value greater than 25% above the average surface hydrophilicity value were defined a...