PEPCAT - A New Tool for Conformational Analysis of Peptides

Abstract

We report a new technique for the efficient analysis and visualization of peptide and protein conformations and conformational relationships, which we have implemented in a computer program called PEPCAT. PEPCAT (an abbreviation for Peptide Conformational Analysis Tool) provides a simple, graphical, and flexible framework that allows the user to define a specific structural feature or juxtaposition of amino acids and to follow the fate of the motif during a molecular dynamics simulation. Here we describe the PEPCAT analysis of the effects of environmental and chemical modifications on conformational preferences of a regulator of hemopoiesis, namely the pentapeptide pyro-EEDCK, and of a confo..