A quadratic approximation for protein sequence to structure mapping

Abstract

A method is proposed to predict the distances between given residue pairs (between Cα atoms) of a protein using a sequence to structure mapping by indefinite quadratic approximation The prediction technique requires a data fitting in three dimensional space with coordinates of the residues of known structured proteins and leads to a numerical representation of 20 amino acids by minimizing a large least norm iteratively. These approximations are used in distance prediction for given residue pairs. Some computational experience on a test set of small proteins from Brookhaven Protein Data Bank are given.