Discretized models of biopolymer structures can be used not only as approximations of the actual spatial structures but also as a computationally feasible approach to the generic features of the sequence-structure relationships. We review the combinatorics of nucleic acid secondary structures as well as lattice models of proteins, and show how properties such as the existence of extended neutral networks or shape space covering can be explained on this basis.
To appear in Handbook of Computational Chemistry and Biology
A. Konopka, Ed., Marcel Dekker Inc, New York
Keywords: Spectral analysis, Fast Fourier transform, Walsh functions, Cayley graphs, fitness landscapes, assignment problems, RNA folding.
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