Figure 1
From: Rapper tk: a versatile engine for discrete restraint-based conformational sampling of macromolecules
The central search algorithm in Rapper is a blend of genetic algorithm and branch-and-bound approach (GABB). Red nodes represent restraints-violating conformation extensions and green nodes stand for the restraints-obeying ones. Some conformational extensions may be left unsampled (not shown). Subtrees emanating from green nodes only are explored further. Set of green nodes at each level is kept below a fixed size (population size), and this allows conformational exploration in time proportional to protein length, leading to an ensemble of restraints-satisfying conformations.