The results of an analysis provides me with a number of 15 amino acid peptides from bacterial proteins. I want to rapidly screen these for those that are most likely to be surface-exposed in the tertiary structure of the protein.
Do you know of a robust mechanism for achieving this? Is a measure of hydropathy the best I can do? Is there a rapid way, assuming a 3-dimensional model, of defining if a particular stretch of residues is surface-exposed? (preferably a non-visual, scriptable means)