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Showing 1 to 20 of 42 for “"RMSD"”.
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A comparison of kernel equating and item response theory true score equating
… error of each equating line is summarized with RMSD. 180 RMSD values in 60 conditions are categorized into 20 general conditions. RMSD values in each level of the general condition are compared with RMSD. All findings have led to the conclusion that KE CE is the superior equating method for all …
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Application of molecular mechanics polarization to fragment based drug design.
… the results the amount good docked poses (< 2 Å RMSD) by up to 12%. However some ligands were bound in incorrect poses. Further investigation was carried out with MD to observe if given enough time ligands bound in an incorrect pose would return to the binding site. In the first stages of …
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An Empirical Investigation of Characteristics of Children's Physical Activity Recall
… In addition, Root Mean Square Difference (RMSD) and Mean Signed Difference (MSD) indexes and the Bland and Altman plots were calculated for determining the effectiveness of physical activity recall. The results showed that accuracy of children's physical activity recall was affected by two …
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Accurate Docking is Achieved by Decoupling Systematic Sampling from Scoring
… SKATE was able to sample poses within 2 Angstrom RMSD of the native structure for 97% of the cases. The best performing scoring function was able to rank a pose that is within 2 Angstrom RMSD of the native structure as the top-scoring pose for 83% of the cases. Compared to published data, SKATE …
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Multiple Alignment of Structures using Center of Proteins
… the widely used root mean square deviation (RMSD) as measures of structural similarity, and the execution time. Some chosen results, from our extensive experimentation, and their significance have been discussed. A web server has also been implemented for trying out a pairwise alignment …
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Methodology Development and Investigation of Turbofan Engine Response to Simultaneous Inlet Total Pressure and Swirl Distortion
… matched within approximately 1% and 2.5° (RMSD), respectively. Experimental turbofan engine ground test results indicated that the ScreenVane manufactured distortion profile matched the predicted S-duct turbofan engine inlet manufactured distortion profile with excellent agreement in …
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Molecular Dynamics Simulations Provide Insight into Stability of Hyperthermophilic Endoglucanases
… contribute to thermostability in endoglucanases. RMSD, RMSF, PCA, hydrogen bonding and salt bridges were analyzed. Finally, protein energy networks were constructed from nonbonded interaction potentials and analysis was performed using hub population, cluster population, largest community …
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Biomolecular Solid-State Nuclear Magnetic Resonance Methods for Spectral Assignment and High-Resolution Structure Determination of Proteins
… in the highest resolution (0.31 A backbone RMSD) protein structure so far determined by SSNMR.
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The Atom Surface Site Interaction Point Approach to Non-Covalent Interactions
… good systematic prediction of phase transfer (RMSD of 5.2 kJ mol<sup>-1</sup>). To consider interactions between two small molecules, we developed a custom pairing algorithm which identifies AIPs that are interacting at molecular interfaces and calculates the free energy of binding by summing …
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A Comparison of Kernel Equating and Traditional Equipercentile Equating Methods and the Parametric Bootstrap Methods for Estimating Standard Errors in Equipercentile Equating
… errors, and root mean squared difference (RMSD) were used as measures to compare the methods to the criterion equating. The results show that KE and its traditional analogues are comparable under the EG design. However, under the NEAT design for which populations were created substantially …
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Comparative modeling of mainly-beta proteins by profile wrapping
… for this fold (ill cross-validation: average C0 RMSD of 1.55 A in accurately wrapped regions, with 88% of the residues accurately aligned). In addition, BetaWrapPro outperforms other fold recognition methods, recognizing the .l-helix fold( with 1]00% sensitivity at 99.7% specificity in …
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Structural studies of amyloid fibrils using solid-state NMR
… monomer structure to generate a high resolution (RMSD of 1.0 Å) of the TTR protofiliment. A disease associated mutant (L 11 M) of these fibrils was also studied by solid-state NMR to determine the monomer structure. Distance measurements on this system were done via 3D TEDOR and R2W, and torsion …
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High Frequency Modeling and Experimental Analysis for Implementation of Impedance-based Structural Health Monitoring
… be handled statistically. A modification of the RMSD damage metric has also been proposed that is essentially the squared sum of the Z-statistic for each frequency point. Preferred excitation frequencies for macro-fiber composite (MFC) active sensors are statistically determined for a long …
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Multi-Property Internal Flow Field Quantification using Molecular Filtered Rayleigh Scattering
… data collected over the entire plane show RMSD values comparable to predicted measurement uncertainties of 0.043 kg/m^3 and 4.0 kPa, respectively. For the same comparison, temperature measurements show a greater RMSD than the predicted uncertainty of 8.4 K. While additional work remains to …
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Solid-State Magic-Angle Spinning NMR Methods for Tensor Measurements and Protein Structure Refinement Using Chemical Shift Tensors
… improved the precision (∼0.3 A backbone RMSD) and accuracy (∼1.1 A related to the crystal structure) of structure determination for GB1. These results demonstrate that de novo structure calculations utilizing Calpha CST data can yield atomic-resolution structures of solid proteins.
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Biophysical Characterization of the Interaction between the Universal Stress G4LZI3 protein and Schistosoma mansoni Hsp60 Substrate Binding Domain
… simulations analysis done in the study include RMSD, RMSF, RoG, SASA and Hydrogen bonding. Additionally, a sufficient amount (11.634 mg/ml) of recombinant G4LZI3 protein was successfully expressed and purified to homogeneity. SmHsp60 was also successfully expressed in the present study. Results …
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Application of Ab Initio Calculations and Molecular Dynamics to Collagen and Brome Mosaic Virus
… as measured by root-mean-square-deviation (RMSD) of coordinates relative to the starting structure and radius of gyration (Rg) of coordinates but that differences still exist in the trajectories and details of the structures. We conclude that more system specific charge parameters are …
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Computational approaches to fragment based screening
… experiments on over 5000 structures. RMSD analysis resulted in many examples of clear improvement for including polarization.
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Structural Studies of Amyloid-β Fibrils using Magic Angle Spinning Nuclear Magnetic Resonance and Dynamic Nuclear Polarization
… the core ranges from Q15-V40 with a backbone RMSD of 0.6 ± 0.1 Å. We proceeded to explore state-of-the-art MAS NMR methods in ultra-fast spinning ¹H-detection (ωr/2π = 111kHz) and fast-spinning high field DNP on fully protonated M₀-Aβ₁₋₄₂ fibrils, whose structure has been thoroughly …
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A fully microfabricated two-dimensional electrospray array with applications to space propulsion
… with 10 µm RMS alignment accuracy and 1.3 µm RMSD repeatability, allows the extractor die to be reused with multiple emitter dies, and potentially with different emitter concepts than the one presented. The thruster, weighing 5 g, was tested with the ionic liquids EMI-BF4 and EMIIm. Time of …
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