A protein folding potential that places the native states of a large number of proteins near a local minimum.

ABSTRACT:

Background

We present a simple method to train a potential function for the protein folding problem which, even though trained using a small number of proteins, is able to place a significantly large number of native conformations near a local minimum. The training relies on generating decoys by energy minimization of the native conformations using the current potential and using a physically meaningful objective function (derivative of energy with respect to torsion angles at the native conformation) during the quadratic programming to place the native conformation near a local minimum.

Results

We also compare the performance of three different types of energy functions and find that while the pairwise energy function is trainable, a solvation energy function by itself is u

SUBMITTER: Chhajer M 

PROVIDER: S-EPMC126205 | biostudies-literature | 2002 Aug

REPOSITORIES: biostudies-literature