Molecular dynamics of associative memory hamiltonians for protein tertiary structure recognition

Abstract

A class of associative memory Hamiltonians for protein tertiary recognition was recently introduced by us. By using a minimization scheme based on molecular dynamics with simulated annealing, we are able to improve and expand upon those initial results. For small proteins lower bound estimates of the Hamiltonians' capacity (the maximum size database for which the Hamiltonian has the ability to reproduce structures) are given; in addition, studies of the dependence of this capacity on various global parameters, such as the choice of sequence encodings, the rate of tolerable mutations in the sequence, and the range of active interactions, are reported. The introduction of the molecular dynamics procedure also permits estimates of the capacity for medium-sized proteins (125–200 residues) to be made. These results demonstrate that the capacity for the simplest realizations of the associative memory Hamiltonians grows as 0.5-0.7N, where N is the number of amino acid residues of the protein to be recalled.