Figure 2.

Available reaction types and their corresponding pattern matching rules. The wildcard character ‘?’ is always shown as a connected dotted line, although depending on context it may represent a non-connected substructure. Domains that change their configuration according to the corresponding pattern matching rule are shown as straight, green, directed arrows. (a) Unimolecular binding. (b) Unimolecular opening. The pattern matching rule is the exact reverse of unimolecular binding. (c) Bimolecular binding. The pattern requires a more explicit formulation than unimolecular binding to ensure a well-formed kernel representation of the product complex. (d) Three-way branch migration. Two distinct rules are necessary to describe the forward and reverse reaction. The patterns for the product of the forward reaction and for the reactant of the reverse reaction are circular permutations. (e) Four-way branch migration. One rule describes both forward and backward reactions, as the reactant pattern is a circular permutation of the product pattern.