Ramachandran basin

By dealing with the evolution of constraints (i.e., Ramachandran basins) rather than the backbone torsional coordinates themselves, the dynamics are judiciously simplified [31]. The algorithm consists of a stochastic simulation of the coarsely resolved dynamics, simplified to the level of time-evolving Ramachandran basin assignments. An operational premise is that steric restrictions imposed by the side chains on the backbone may be subsumed into the basin-hopping dynamics. The side chain constraints define regions in the Ramachandran map that can be explored in order to obtain an optimized pattern of nonbonded interactions. 

Fig. 3.3 Internal energy and number of hopping residues along a reproducible representative FM trajectory for the thermophilic variant of protein G. A hopping residue is defined as tagged for a Ramachandran basin transition in the coarse-grained stochastic process that underlies the FM torsional dynamics. Reprinted from [35], with permission from Elsevier...

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