One embodiment of the present invention is directed to a method and system for designing the monomer sequence of a polymer to produce a particular polymer that adopts an initially specified, 3-dimensional conformation in a specified chemical environment. In one specific embodiment, the method and system produces amino-acid sequences for polypeptides in order to generate polypeptides that adopt initially specified, 3-dimensional conformations. Additional embodiments determine sequences for various other types of biopolymers in order to produce biopolymers that adopt specific conformations in specified chemical environments. For example, these method embodiments may be used to design sequences for polysaccharides, polynucleotides, and hybrid biopolymers.