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We achieved an average CA-RMSD of 10.94 Å for initial structure generated by ab initio models, which improved slightly with energy minimization step (10.77 Å).
For initial structure, bixbyite In2O3 supercells containing 80, 130, or 180 atoms and with a density of 7.12 g/cm were used.
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Ramanavicius et al (15) reported that using their potential pulse technique with a range of 0.6 to 1.2 V versus Ag/AgCl for initial structuring of the Ppy was most suitable for entrapping biologically active materials.
For initial structure-activity relationship (SAR) comparison studies of the naturally derived codonopsinine, some chemical modifications on the respected derivatives were performed which include installation of different substitution on the aromatic ring (except compounds 12e 16e).
Dynamics were run as described above for the initial structure generation except that simulations were run for a total of 30 ns.
The NO3 increased significantly from 26.8% for the initial structure to values ranging between 78.6 93.3% for the interpolation-based models, with the highest values achieved again by IDW (Fig. 4).
Since Confab does not explore ring conformations, ring conformations were taken from the crystal structure for the initial structure generation.
The success of this simulation was strongly dependent on the findings for an initial structure between the apo-LBD and the ligand as well as the discovery of the driving forces underlying the ligand-trapping and subsequent ligand-induction processes.
Bomis originally planned to make Wikipedia profitable, providing staffing and hardware for its initial structure; Wikipedia would not have survived without this early support.
The in-house X-ray diffraction data, processed to 2.2 Å resolution, were used for the initial structure solution and refinement, and the higher-resolution synchrotron data were used for refinement of the final model.
Experimental phases for the initial structure determination were obtained from Single Anomalous Diffraction (SAD) experiments on crystals grown from selenomethionine-derivatized proteins by using the software package PHENIX (Adams et al., 2002).
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