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. 2013 Aug 29;9(8):e1003209. doi: 10.1371/journal.pcbi.1003209

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© 2013 Dehouck, Mikhailov

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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The accuracy of the estimation of pairwise residue fluctuations by different ENM variants is illustrated on the basis of two individual proteins. For each protein, 20 randomly selected residue pairs (10 with Å, and 10 with Å) are connected by solid lines. A green line indicates that the amplitude of the fluctuations of the interresidue distance is well estimated by the model. A red (blue) line indicates that the amplitude of the fluctuations of the interresidue distance is largely overestimated (underestimated) by the model. Values larger than 100% or lower than −100% are assimilated to 100% and −100%, respectively. In addition, for each protein and each ENM variant, we report the error on the estimation of pairwise fluctuations (eq. 15), which accounts for all pairs of residues in the protein. (A,C,E) High quality structural ensemble of ubiquitin, obtained by combining NMR information with molecular dynamics simulations (PDB: 1xqq) [38]. (B,D,F) NMR structural ensemble of periplasmic chaperone FimC (PDB: 1bf8). The relatively rigid orientation of the two domains is ensured by specific interdomain interactions [39]. (A–B) . (C–D) . (E–F) .

Inline graphic — The accuracy of the estimation of pairwise residue fluctuations by different ENM variants is illustrated on the basis of two individual proteins. For each protein, 20 randomly selected residue pairs (10 with Å, and 10 with Å) are connected by solid lines. A green line indicates that the amplitude of the fluctuations of the interresidue distance is well estimated by the model. A red (blue) line indicates that the amplitude of the fluctuations of the interresidue distance is largely overestimated (underestimated) by the model. Values larger than 100% or lower than −100% are assimilated to 100% and −100%, respectively. In addition, for each protein and each ENM variant, we report the error on the estimation of pairwise fluctuations (eq. 15), which accounts for all pairs of residues in the protein. (A,C,E) High quality structural ensemble of ubiquitin, obtained by combining NMR information with molecular dynamics simulations (PDB: 1xqq) [38]. (B,D,F) NMR structural ensemble of periplasmic chaperone FimC (PDB: 1bf8). The relatively rigid orientation of the two domains is ensured by specific interdomain interactions [39]. (A–B) . (C–D) . (E–F) .