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Applying rigid transformation protocols, population of the detected domain building models with an average root mean square deviation from native structures of 2.3 Å and an average template modeling score from native structures of 0.43 has been obtained.
In general, the degree of deviation from native speech and the incidence of disfluencies will be in inverse relation to the degree of proficiency in the target language.
The parameters of the orientation-dependent functions were optimized so that decoy proteins with low RMSD (root mean square deviation) from native structures could be distinguished from a pool of decoys (obtained by perturbing the energy functions and then modeling the entire protein).
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Deviations from native valve hemodynamics can result in an increased Reynolds Shear Stress (RSS), which has the potential to instigate hemolysis or shear-induced thrombosis.
Thermodynamic parameters in Table 1 are differential thermodynamic parameters; i.e., they represent deviations from native DNA duplexes.
Such deviations from native protein geometry may be loosely viewed as an implementation of the minimax principle from game theory: select the conformation that minimizes the maximal possible loss in the case of failure.
A local refinement of the native GC pilus structure was applied, and the results also show a deviation from the native structure, which is correspondent with the results in the last section.
On average, the representative set of rebuilt structures best satisfying the constraints imposed by the five types of interhelical interactions has an average Cα root-mean-square deviation from the native of 1.03 Å. Implications for protein folding, structure and motion prediction, modeling, and design are discussed.
The lowest energy structure showed a large deviation from the native structure (4.61 Å).
Among the different categories, the spH1 H-atoms have the largest deviation from the native position, and all three methods failed to achieve an average RMSD below 1.0 Å.
We should note on passing, that the value obtained for ΔΔGfolding using the rms deviation from the native state as an order parameter (Fig. 5) is higher (but comparable) with the value obtained from the dihedral principal component analysis (Fig. 4) which gives a value of ΔΔGfolding[truncated-native] of +5.7 kJ/mol (at 320 K).
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CEO of Professional Science Editing for Scientists @ prosciediting.com