Representation and modeling of protein surface determinants

Surface characterization of peptides may provide useful information about functionality and potential interactions with other molecules. A description of a protein site through a surface that models the shape conferred by the exposed residues is an effective tool for the analysis and the modeling of proteins that may highlight similarities and relationships not detectable through comparisons at level of primary, secondary, and tertiary structure. This study concerns the development of a tool that extracts the residues that concur to the shape modeling of the surface of a protein or a portion of it. This task is accomplished without taking into account the order of the amino acids in the primary structure, but only according to the selection of a portion of the protein indicated through geometric parameters or an explicit list of amino acids belonging to the site of interest. Both in the case of an entire protein and in the case of a portion of it, the method provides the mesh that models the surface described by the exposed residues that constitute the external envelope. The developed tool which allows the extraction of the exposed residues, and thus of the potential function determinants, is applied to identify the amino acids that concur to the structural interaction in several protein complexes.