Patent ID: 7437336

Claim:
A computer-implementable method for finding multiple solutions to a physical problem relating to computational biology, said method implemented using a set of instructions storable in a computer memory upon which execution of said instructions causes a computer to perform the actions comprising: a) modeling said physical problem as an objective function, said objective function configured for mapping structures in a search space having a multitude of points by defining a distance metric over said search space, wherein input data for said distance metric is specific to protein folding, the data comprising structural distance measurement data between corresponding atoms; b) generating a multitude of candidate solutions for said objective function; and c) for each of said candidate solutions at each of said multitude of points, determining a set of acceptable and distinct solutions by: i) calculating a fitness using said objective function, wherein said fitness is scaled to maintain a selective pressure; ii) assigning each of said fitness to its candidate solution; iii) transforming said fitness using a penalty function; iv) determining if said candidate solution is acceptable; v) determining if said candidate solution is sufficiently distinct; and vi) adding said candidate solution to said set of acceptable and distinct solutions if said candidate solution was determined to be acceptable and distinct.