This process of automatic- and manual model refinement steps was iterated until no further improvement on both Ramachandran geometry and R-factors was evident.
For the model combination and refinement step of our pipeline, we used a novel global local model combination algorithm.
The previously published genome-scale model for R. sphaeroides iRsp1095 [ 11] was used as the starting point for a 2-step model refinement.
The second step was model refinement.
In a second step of model refinement, putative enzymes capable of catalyzing reactions added to iRsp1095 where identified by BLAST searches using the protein sequences from other organisms previously verified to carry out the reaction in question.
Model building and refinement steps were performed with PHENIX suite and COOT.
Out of these models, the highest ranked 3D pharmacophore displayed the best results in an initial model validation and was selected for a step-wise model refinement.
After evaluating several existing model refinement and model reduction/expansion techniques, a two-step damage detection approach was developed for large structures with limited instrumentation.
