Similarity study on peptide gamma-turn conformation mimetics

The ability of a series of structures to mimic the geometric and electronic properties of an ideal gamma-turn has been studied. Initially, an exhaustive conformational analysis was carried out using the molecular dynamics technique at high temperature followed by minimization. Additionally, each minimum was optimized with the semi-ab initio molecular orbital method SAM1. Then, the unique minima found have been superimposed with ideal gamma-turns, classic and inverse, using the SEAL program which takes into account steric and electronic parameters for the superpositions and finally, three molecular similarity indices were determined for each superposition. These indices consider the general steric and electronic characteristics of the structures, as well as, the position of the carbon atoms that correspond to the C alpha(i) and C alpha(i+2) in the peptide chain.