CONFLEX: Conformational Behaviors of Polypeptides as Predicted by a Conformational Space Search

摘要

A new method for searching folding pathways of small polypeptides from over thousands conformers, which were generated by our original Conformational space search program, CONFLEX, has been developed. In order to approximate an interconversion between similar conformers, Conformational distance in an angular space based on all peptide's back-bone torsion angles (φ and ψ) were used as a Conformational similarity index. A folding pathway that consists of a series of conformers between predefined starting and target conformers was determined by using a single-linkage clustering technique based on the similarity indices of Conformational distance matrix. This method has been applied to finding a folding pathway from seven thousands conformers of alanine octamer. Interesting Conformational behaviors in this folding process have been discussed.