The present invention provides a method and apparatus to significantly accelerate the searching process based on the Monte Carlo principle and the lattice model. Specifically, the energy status of a lattice-based protein conformation is evaluated by modeling the folding process through a pipelined digital circuit using a number of state machines. The pipelined digital circuit reduces the time required for the determination of the energy status of a particular conformation and, therefore, significantly accelerates the searching speed for the lowest energy status. The present invention also permits real-time tuning of problem parameters by the experimenter.