Mining combinatorial data in protein sequences and structures

Combinatorial searches of structural and physical chemical properties involving the components of libraries of dipeptide, tripeptide and tetra peptide fragments were carried out in the Protein Data Bank and the SwissProt databases. The properties investigated are structural propensities, co localization of peptide fragments in protein sequences, interactions between peptide fragments in close structural proximity and the participation of physical chemical profiles in the distribution of structural motifs among peptide fragments. The results obtained for each combinatorial search in the study are classified according to the structural motifs alpha-helix, beta-sheet, reverse turn I and reverse turn II. The application of combinatorial data mined in protein databases to the design of new peptide libraries is discussed. The present findings have implications for the study of protein structure which are also discussed.