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Figure 1 | BMC Bioinformatics

Figure 1

From: Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations

Figure 1

ConTemplate results demonstrated using the S100A6 Ca2+ binding protein. The Ca2+-free (A) and -bound (B) conformations are shown in the upper panels; helix 3 is marked in red, and the calcium ions in magenta. C. Reproducing the Ca2+-bound conformation, starting from the Ca2+-free conformation as a query. The maximal RMSD between the query and similar proteins is set to 1.2Å, the minimal Q-score to 0.4, and the number of clusters is set to 2. D. Reproducing the Ca2+-free conformation, starting from the Ca2+-bound conformation as a query. The similarity cutoffs are the same as in C, the number of clusters is set to 17.

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