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. 2019 Jan 31;20(3):606. doi: 10.3390/ijms20030606

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© 2019 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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Sampling scheme of the CABS model. Blue panels show implementation details of Monte Carlo (MC) iterations (loops). The orange panel shows all motions that may be performed in a single MC step. The simulation is organized as a set of nested loops, in which the s number of MC steps is organized into the y number of cycles, and these in a annealing cycles (number of a, y or s cycles can be controlled by the user in CABS-flex and CABS-dock standalone packages [72]). In the orange panel, numbers 1 to 5 denote the available moves, presented together with the number of attempts to perform a move in each of the MC steps. The resulting trajectory is comprised of simulation snapshots saved at the end of each MC cycle.