An optimal procedure to extract interaction potentials for protein folding

Abstract

A formidable challenge in molecular biology is the prediction of the three-dimensional structures of the native state of proteins from their sequence of amino acids. An essential step to solve this problem is the extraction of the coarse-grained interaction potentials between the amino acids. Here we outline preliminary results of a strategy that accomplishes such goal with the search of those potentials which are able to recognize the native state of a protein as a stable local minimum. The method is implemented by exploiting several numerical and analytical tools which have been recently developed by our group. The results are extremely promising: despite the fact that we have used simple forms for Hamiltonians, the extracted potentials are able to stabilize simultaneously at least 10 proteins of different classes to an average distance (per residue) less than 3 Å from the native state.