Discrete Models of Biopolymers 2

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 combi-natorics 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. D Number of neighbors. Sometimes written as D = D(n). a Alphabet size. Scaling exponent EEective lattice connectivity d Distance, lattice connectivity (distinction clear from context) z Lattice connectivity E Expected value Measure (d) Number of forward neighbors at distance d. Fraction of neutral neighbors A constant arising in RNA structure counting. a sequence space with alphabet size a and sequence length n. matrices in boldface chemical stuu in sans serif greek uppercase ?; ::: for random (induces sub-)graphs fraktur font: reserved for higher level constructions such as probability spaces of random graphs, Voronoi cells.