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. 2017 Feb 7;7:41364. doi: 10.1038/srep41364

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Copyright © 2017, The Author(s)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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ZDOCK docking procedures simulate the interaction between Smurf2 and Nedd8, set HECT domain (PDB code: 1ZVD) for the acceptor, Nedd8 (PDB code: 1XT9) is docked ligands. ZDOCK evaluated according to the geometry of the surfaces of the two molecules, hydrophobicity and polarity of the degree of matching. In total, the combination of two modes is shown in (A,B). Smurf2 and Nedd8 binding mode 1 is shown in (A) (overall view): N-lobe Small domain binding to Nedd8; different proteins and different regions are marked with different colors. The second mode is the C-lobe and details are shown in (B).