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Figure 2 | BMC Bioinformatics

Figure 2

From: A replica exchange Monte Carlo algorithm for protein folding in the HP model

Figure 2

VSHD Moves. Residue positions are shown before the move and immediately after a successful move. T(t) denotes the state of the conformation at time t. In 2a there are two possible positions that residue one could be moved to, denoted by 1' in grey circles. Each position is checked in random order for availability. If a position is found to be free, the residue is moved. In 3D the same logic is followed except there is a possibility of two additional potential positions (four in total). End moves are applied on the last residue n in the same manner. 2b shows there to be only one potential new position for a corner move. This is also the case in 3D where the position must lie on the plane formed by i - 1, i, and i + 1. 2c shows the case for a crankshaft move. In 3D, the crankshaft could potentially rotate 90° or -90°.

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