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. 2011 Jun 14;27(13):i52–i60. doi: 10.1093/bioinformatics/btr248

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 5. — Synthesized conformations from QAARM reveal novel binding modes of ubiquitin substrate. (A) A movie-like representation of the fluctuations in ubiquitin synthesized from the QAARM model. Note that regions undergoing large conformational changes include the binding regions and the ancillary regions of ubiquitin. These motions have a direct implication on binding a variety of substrates. (B) Synthetically generated 25 000 conformers are projected back onto the QAA bases to reveal the number of potential contacts that each of the synthesized conformer can make with a known substrate, Rabex 5. Note that the substate highlighted by the ellipse consists of a small number of conformers in the synthesized data that can form a large number of contacts with Rabex 5.