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 Angstrom from the native
state.
