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0003096681
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edited by M. F. Thorpe and P. M. Duxbury (Plenum, New York)
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D. J. Jacobs, L. A. Kuhn, and M. F. Thorpe, in Rigidity Theory and Applications, edited by M. F. Thorpe and P. M. Duxbury (Plenum, New York, 1999), pp. 357-384.
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33645049995
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note
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The entropy loss from a redundant constraint is expected to be a small fraction of what would occur if the constraint was independent. Accounting for this second-order effect is possible at the expense of losing simplicity.
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28
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33645051341
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note
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The DCM explicitly neglects relaxation within constraints. Relaxation in structure can be described by incorporating more geometrical bins at the expense of losing simplicity.
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32
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0037441653
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S.C. Lovell, I.W. Davis, W.B. Arendall, III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson, Proteins 50, 437 (2003).
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Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
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33
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33645078273
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note
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The propagation rule was applied from left to right and right to left on 200 000 chains with length of 100 000 as well as millions of chains of lengths ranging from 10 to 1000 all having random conformations. These results were compared to exact calculation using the pebble game per framework. Agreement between all three results was always obtained.
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34
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33645075324
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note
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s and the special matrices {S, R, Q} required expanding the dimension of the direct product space. The dim(T) referes to the subspace that excludes the s state.
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35
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33645071819
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Donald J. Jacobs and G. G. Wood (unpublished)
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Donald J. Jacobs and G. G. Wood (unpublished).
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39
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33645056070
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note
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The objective of finding an optimal set of parameters with available data in the literature is outside the scope of this work. The subject of obtaining an accurate DCM parametrization is deferred to future work.
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43
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0001248516
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M.F. Thorpe, D.J. Jacobs, M.V. Chubynsky, and J.C. Phillips, J. Non-Cryst. Solids 266-269, 859 (2000).
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Phillips, J.C.4
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47
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33645091372
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note
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A third parameter called u in the LR model is arbitrarily set to unity, which is analogous to the arbitrary choices made in fixing some DCM parameters.
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52
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0034533671
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M. Carrion-Vazquez, A.F. Oberhauser, T.E. Fisher, P.E. Marszalek, H. Li, and J.M. Fernandez, Prog. Biophys. Mol. Biol. 74, 63 (2000).
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Fernandez, J.M.6
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53
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33645048066
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D. Huynh, S. Dallakyan, and D. J. Jacobs (unpublished)
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D. Huynh, S. Dallakyan, and D. J. Jacobs (unpublished).
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