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. Author manuscript; available in PMC: 2016 Jun 1.
Published in final edited form as: Proteins. 2015 May 8;83(6):1151–1164. doi: 10.1002/prot.24808

Fig. 5. Rotamer Partitioning Scheme and Benefits of Partitioned Rotamers.

Fig. 5

A) An example of how a rotamer is partitioned. In this example the rotamer r with two dihedrals is first partitioned along the χ1 dimension to create two new rotamers r1 and r2. Next the partitioned rotamer r1 is further split along the χ2 dimension to create the partitioned rotamers r1a and r1b. B) In the original iMinDEE protocol, as conformations are enumerated the pairwise bounds are never updated so E⊖(ℓ) remain constant. However, during a partitioned rotamer design the bounds are updated, which increases E⊖(ℓ) during the run. Since the iMinDEE I value is defined as I = ET (g′) − E⊖(ℓ), the Im+1 value continuously shrinks during the partitioned rotamer conformation enumeration, allowing for additional rotamers to be pruned as more rotamers are partitioned.