Models along this continuum represented intermediate spatial models (same way as the intermediate models described before) between target and gaze models in eye-centered coordinates (see Results; Fig. 10).
The similarity between target and candidate model is measured by the discrete formulation of the Bhattacharya coefficient: (16).
There have been many reports about the relationship between target modeling methods and hit ratios (Bissantz et al 2003; Diller and Li 2003; McGovern and Shoichet 2003; DeWeese-Scott and Moult 2004; Oshiro et al 2004; Nicholls 2008; Sheridan 2008).
Because of the low sequence similarity between target and template, a rigorous iterative modelling protocol was adopted in which 50 models were constructed and analysed.
In consequence of this high degree of similarity between target and template sequences, the molecular model of G. diazotrophicus nitrogenase complex presented high stereochemical quality.
However, when a target is occluded, the conventional KT tends to lose the tracked target because of mismatch between target model and target candidate.
For two considered distribution, according to eq. (6), distance between target model and target candidate will be as: dleft overrightarrow{y}right)=sqrt{1-rho left overrightarrow{p}left overrightarrow{y}right),overrightarrow{q}right)} (8).
As shown in Figure 1, local lDDT scores are not dominated by different domain orientations between the target and the model structures, but correctly reflect the accuracy of the local atomic environment surrounding the residue under investigation in the model.
The evaluated Ramachandran plot for the modeled proteins were also compared to the template proteins (1XCQ and 1 N64) to check the distribution of residues in favored and disallowed regions between each target and template models.
Also, a subroutine was developed in Wolfram Mathematica (Wolfram Research, Inc., Mathematica, Version 8.0.4.0) to observe and assess the regions of asymmetry, and the regions with a deviation higher than 1 mm between the target and reference models were automatically isolated using the DCMs.
