Figure 2
From: SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design
Screenshot of SUPERFICIAL displaying the options. Sections A and B are the same for all submenus/menu items ("load protein", "show", "options" and "peptide"). Section A gives a short description of the options and may act as a guide for the user. In section B the subsequent results of the settings are shown and the user may check the effects on the size of the surface and the peptides. The options in C determine the surface of a protein, whereas the first entry ("percentage of atoms at surface per amino acid") has the greatest influence on the surface extension. Section D gives the definitions for peptide generation. All changes are visualised in B on sequence level. The whole protein is displayed in the submenu "show" (Fig. 3).