An example where the template has a low structure similarity to the query.

<p>This case demonstrates that using less similar templates still has the potential to produce satisfied results. This figure contains two proteins that share similar DNA-binding interface but have low global structure similarity (TM-score = 0.38). The <i>Ψ</i>-score of the predicted PWM to the annotated PWM using the orange protein (1MH3:A, MATA1_YEAST) as the query and the green protein (1SKN:P, SKN1_CAEEL) as the template is 0.18. Contact residues on both protein structures are plotted in <i>sticks</i> presentation.</p

Predictions by the proposed method on the seven test cases.

<p>The predictions of the proposed method are denoted as ‘Unbound’, in comparison with the annotated PWMs (‘Annotated’), the predicted PWMs based on native complexes (‘Native’) and the complexes of homologues (‘Naïve’). (A) PWMs. (B) A position is marked as ‘•’ if its most favorable base type was correctly predicted, or marked as ‘–’ otherwise. (C) <i>Ψ</i>-scores and the corresponding p-values. The value within the parentheses of the first column indicates the average <i>Ψ</i>-score.</p

Predictions using unbound structures compared with those using native complexes.

a<p>data from Xu <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030446#pone.0030446-Xu1" target="_blank">[12]</a>.</p>b<p>data from Morozov <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030446#pone.0030446-Morozov1" target="_blank">[10]</a>.</p>c<p>our implementation, which is a variation of FIRE.</p>d<p>the unbound structures and the corresponding templates used were listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030446#pone-0030446-t002" target="_blank">Table 2</a>.</p

The three synthetic complexes employed in the analysis of structural variations.

<p>The three synthetic complexes employed in the analysis of structural variations.</p

Structural transitions upon DNA-binding.

a<p>SSE: transition of secondary structure.</p>b<p>D2O: disorder-to-order transition.</p>c<p>RMSD: root mean square deviation.</p

The PDB entries used in this study.

a<p>native complexes of the corresponding proteins.</p>b<p>unbound structures of the corresponding proteins.</p>c<p>native complexes of different proteins used as the templates.</p

The validation set used in this study.

a<p>UniProt entry name.</p>b<p>not used in the study of Morozov <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030446#pone.0030446-Morozov1" target="_blank">[10]</a>.</p>c<p>containing two chains of different proteins.</p

Predictions using different complexes.

<p><i>μ</i>: the proposed method. <i>U</i>: the second synthetic complex that eliminates the second type of structural variation. <i>B</i>: the third synthetic complex that eliminates the second and third types of structural variation. <i>N</i>: native complexes. (A) PWMs. (B) A position is marked as ‘•’ if its most favorable base type was correctly predicted, or marked as ‘–’ otherwise. (C) <i>Ψ</i>-scores and the corresponding p-values. The value within the parentheses of the first column indicates the average <i>Ψ</i>-score.</p

Comparison with predictions of using docking to construct synthetic complexes.

<p>The predictions based on the proposed alignment-based approach to construct synthetic complexes are denoted as ‘Alignment’, while those of ZDOCK are denoted as ‘Docking’. (A) PWMs. (B) A position is marked as ‘•’ if its most favorable base type was correctly predicted, or marked as ‘–’ otherwise. (C) <i>Ψ</i>-scores and the corresponding p-values. The value within the parentheses of the first column indicates the average <i>Ψ</i>-score.</p

Demonstration of base substitution.

<p>This case demonstrates the ability of the employed all-atom potential function to replace the base types when the native DNA sequence in the selected template is not the same as the target DNA sequence to that the query protein can bind. A position is marked as ‘•’ if its most favorable base type was correctly predicted, or marked as ‘–’ otherwise. In addition, the symbol ‘↑’ stands for a successful substitution. The sequence shown is the DNA sequence in the selected template, where red nucleotides indicate the positions of which the bases are different to the most favorable base types in the annotated PWMs.</p