Patent ID: 7574306

Claim:
A method, carried out on an electronic computer, for determining a monomer sequence for a polymer in order to produce a polymer that adopts a specific, predetermined 3-dimensional conformation in a specified chemical environment, the method comprising: receiving, by the electronic computer, a specification of a desired 3-dimensional conformation; selecting, by the electronic computer, a number m of initial polymer-backbone conformations, where m is greater than 1; for each of the m initial polymer-backbone conformations, selecting, by an electronic computer, a number n of initial sequences, where n is greater than 1, thereby creating mn threads; iteratively optimizing, by the electronic computer, the polymer-backbone conformations of each thread with respect to an estimated free energy, and optimizing, by the electronic computer, the polymer sequence of each thread with respect to an estimated free energy; and outputting, by the electronic computer, final monomer sequences of a number of threads to a user by listing each of the number of threads in a computer-readable medium or on a display device, the listing indicating, for each of the number of threads, a probability or relative probability that a polymer having a sequence of the thread adopts the desired 3-dimensional conformation.