Backbone conformations, bend structures, helix structures and other tests of an improved conformational energy program for peptides: ECEPP83

Abstract

Improvements in the potentials used in the computer program ECEPP (empirical conformational energy program for peptides) and a variety of test cases using a new program (ECEPP83) are described. The changes made in ECEPP are based on recent results of ab initio geometry optimized dipeptide studies, and also on the inability of ECEPP potentials to predict low‐energy conformations in regions of Ø‐Ø space where experimental β‐bends occur. The concept of the thermal ellipsoid is also developed as a method for visualizing correlated conformational motion about energy minima. A series of previously studied bend structures in proteins are examined again using the improved program, ECEPP83. The changes made to the program are found to result in significant modifications in the ordering of computed energy minima, protein bend structures, and in the values of Ø and Ø at the energy minimum for helical homopolymers. Agreement with experiment is improved over that found using ECEPP.