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Test/analysis correlation, in the refinement of finite element models to accord with test results of the modeled structure is an emerging field in the today's automotive industries.
Hence, the results from the molecular dynamics simulation indicated that the modeled structure is stable.
For the complex, the modeled structure is clearly reminiscent of the collapsed mode of CaM-peptide interaction, and a structure of a CaM-CaMK peptide complex can easily be fitted into the model (Figure 3D).
Since the sequence homology between the PE-PPE domain and known 3-D structures is very low, the validation of the overall fold of the modeled structure is very important.
The above parametric comparison shows that the modeled structure is good for the further analysis like docking, to find some potential inhibitor.
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43 The modeled structure was assessed through SWISS-MODEL structure assessment tool 44 and ANOLEA (atomic non-local environment assessment) 45 assessing the packing quality of the models.
9, 10 The modeled structure was evaluated using PROCHECK, a protein structural quality analysis software.
Further, homology modeling and refinement was performed and the refined modeled structure was used for molecular docking with the immune receptor (TLR-3) present on lymphocyte cells.
The modeled structure was validated by multiple analysis tools.
The modeled structure was refined using energy minimization.
The modeled structure was stabilized using Molecular Dynamics simulations.
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