An Artificial Neural Network Based Approach for Identification of Native Protein Structures Using an Extended Forcefield

Abstract

Current protein force fields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the force fields do not take into account the use of hydrogen bonds which are important for secondary structure creation and stabilization of proteins. SCOPE is an open-source program that generates proteins from rotamer space. It then creates a force field that uses only non-bonded and hydrogen bond energy terms to create a profile for a given protein. The profiles can then be used in an artificial neural network to create a linear model which is funneled to the true protein conformation.