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. 2018 Mar 28;46(8):3852–3863. doi: 10.1093/nar/gky228

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© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 5. — Accuracy on the docking predictions: In all cases cyan colour is used for docked DNA and red for the crystallographic one. (A) TAL effector (PDB: 4jc9), protein–DNA interface regions and nucleotide sequence specificity are correctly predicted. (B) Left and right: Cartoon and VdW surface style for a dimeric structure with DNA (PDB: 1p71; Upper) and the related protein crystallized as a monomer missing part of the structure (PDB: 5eka; lower). Predicted docked DNA in both structures in cyan. (C) histogram of sequence specificity accuracy over 13 proteins of different PFam family. (D) Humanized yeast ACC carboxyltransferase (PDB: 5tct) binding region (zoomed) was found within the five best energy docks. (E) the DNA-directed RNA polymerase subunit alpha of Bacillus subtilis (PDB: 3gfk, grey) superimposed to the overlapping domain of the E. coli ortholog with low sequence identity (PDB: 5ciz chainB, magenta). (F) The helical bundle of AND-1 human protein (PDB: 5gvb) present a dense cloud of docked fragments (left side) in the binding groove formed by the α2 and α4 helices. Within the six best energy docks for AND-1 human protein we found three docks (right side) placed within the predicted binding region.