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KicMover

Generate new backbone conformations for the loop being sampled. Conformations are generated using the kinematic closure (KIC) algorithm. The idea behind KIC is that every time a new conformation is generated, all but 6 of the torsions can be picked however the user likes, e.g. from Ramachandran space (the most common choice), from a fragment library, according to some custom algorithm, etc. The remaining 6 torsions are solved for analytically to ensure that the backbone stays closed and that all bond lengths and angles maintain ideal values. KIC is a very general algorithm, good for building loops from scratch, modeling big conformational changes, modeling small conformational changes, and generating backbone ensembles.

<KicMover name="(&string)" loop_file="(&string)"/>

Right now KicMover is not really customizable at all, but I'm hoping to change this in the near-ish future (current date: November 2014). In particular, I want to add a general way to specify different algorithms for perturbing the torsions, picking the pivots residues, and filtering the solutions. In the meantime though, this mover is pretty static.

Options:

• loop_file: See LoopModeler.

Subtags:

• Loop: See LoopModeler.

Caveats:

• See LoopModeler.

References:

• Mandell DJ, Coutsias EA, Kortemme T. (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature Methods 6(8):551-2.

• Coutsias EA, Seok C, Wester MJ, Dill KA. (2005). Resultants and loop closure. International Journal of Quantum Chemistry . 106(1), 176–189.