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With these refinements implemented in miRNA target prediction, the results of pathway enrichment analysis on the basis of the coregulated targets should provide a good insight into the functional role of dysregulated miRNAs.
Subsequently, the model was rebuilt and refined with COOT58 and phenix refinement implemented in the PHENIX program suite, with the individual anisotropic ADP refinement59.
Block-structured adaptive mesh refinement, implemented with the Chombo framework, is utilized to reduce the computational cost while keeping high resolution mesh around the embedded boundary and regions of high gradient solutions.
Therefore, best compounds achieved through the virtual screening process usually undergo a protocol of energy refinement implemented using molecular dynamics [ 35].
Initial docking of clathrin model segments into the EM density map was carried out manually using the program O (Jones et al, 1991) and improved using rigid body refinement implemented in MAVE.
The resulting model was manually completed in Coot [35] and restrained-structure-refinement implementing TLS refinement [36] resulted in cAMP model with Rwork and Rfree of 20.6% and 23.0% respectively.
Towards the end of the refinement, TLS refinement as implemented in phenix.refine was used [53].
Eight new refinements were implemented in the MODIS Land Surface Temperature and Emissivity (LST&E) product suite when transitioning from version 4 (V4) to version 5 (V5).
These refinements were implemented for the third round of applications.
The refinements were implemented in iAbaylyiv3, increasing global accuracy from 88%to94%4%.
The computer software used in this study was a refined version of the package Diverse [ 25] described in Maddison et al. [ 1], with these refinements already implemented in Mesquite [ 26].
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