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<p><em>..................................................</em></p> <p><em><strong>Figure 1 Accuracy-representative models from the CABS decoys set</strong>. Three 2GU3A example models with various distances from the native structure (the lowest energy model – 0.6 Å, intermediate 1.5 Å, and the worst one 3 Å from native). Models are plotted in gray, reference native structure in dark thin line.<br></em></p> <p><em><img alt="" src="/user_files/Image/Methods/all-atom force field f01.jpg"></em></p> <p><em>..................................................</em></p> <p><em><strong>Figure 2 Illustration of the secondary structure dependent character of differences between the accuracy-representative models</strong>. RMSD deviation from native for each residue of three 2GU3A example decoys (after the best superimposition of the entire structures – see Figure 1). On the sequence axis the secondary structure is symbolically depicted (helices in black and strands in grey).<br></em></p> <p><em><img alt="" src="/user_files/Image/Methods/all-atom force field f02.jpg"></em></p> <p><em>..................................................</em></p> <p><em><strong>Figure 3 Results of 1000 iteration minimization for the CABS decoys</strong>. For each protein, the energy was plotted as a function of C<span>α</span> RMSD for all decoys (left panels) and without decoys with abnormal high energy values resulted from structural inaccuracies (right panels). On the left panels, energies of the native structures are denoted by asterisks. The native structures were subjected to the same rebuilding procedure from the C<span>α</span>-traces as that applied to the decoys. Proteins are ordered in respect to their chain lengths (Table 1) – from the smallest on top (2GR8A) to the largest (2CJPA) on the bottom.<br></em></p> <p><em><img alt="" src="/user_files/Image/Methods/all-atom force field f03.jpg"></em></p> <p><em>..................................................</em></p> <p><em><strong>Figure 4 Results of 1000 iteration minimization for the Moulder decoys</strong>. For each subset of decoys, the energy was plotted as a function of C<span>α</span> RMSD for the best scored decoys.<br></em></p> <p><em><img alt="" src="/user_files/Image/Methods/all-atom force field f04.jpg"></em></p> <p><em>..................................................</em></p> <p><em></em></p>
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