Sentence examples for modeled structures were from inspiring English sources
Structural constraints and prediction quality of the modeled structures were evaluated using WHATIF [ 35] and PROCHECK [ 36].
Modeled structures were subjected to energy minimization and final models presented high-quality local and overall stereochemistry with approximately 98% of amino acid residues lying in allowed regions of the Ramachandran plot.
All the calculations of modeled structures were carried out for 300 K.
Verify_3D showed that the overall scores of the modeled structures were greater than 85 indicating a good compatibility between the 3-D modeled structure and its corresponding 1-D amino acid sequence.
The modeled structures were then re-minimized.
The modeled structures were validated by performing full geometric analysis with Procheck [ 11].
Accuracy of the best obtained models, calculated as coordinate root-mean-square deviation (cRMSD) between the target and the modeled structures, was under 1 Å, which is competitive with experimental methods, such as crystallography or NMR.
Structure refinement of modeled structures was carried out using the Discovery Studio software suite version 3.0 (Accelrys Inc , USA.
Finally, the feasibility of modeled structures was evaluated by Verify3D to ensure that all the predicted structures had an acceptable 3D-1D self-compatibility score.
Splayed-apart views of the contact surfaces for the modeled structures are shown in Figure 7 and further analyses are described in Additional files 13 and 14.
The stereochemical quality of the modeled structures was verified using the PROCHECK 25 and WHAT_CHECK 26 algorithms and by assessment of Ramachandran plots.
