TABLE 1.
Docking poses of the p53‐binding domain of N‐MDM2 to the host structure of PADI4, obtained from different predictors and ranked by using the MM/GBSA technique, with total binding affinity and per‐residue contribution (in parentheses).
| Docking algorithm | Pose rank | Binding affinity (kcal mol−1) | Best contributions to binding affinity (kcal mol−1) | |
|---|---|---|---|---|
| PADI4 | MDM2 | |||
| ClusPro | 1, 2 | −112.33 | Phe634 (−6.99), Thr635 (−5.71), Asp473 (−5.68) | Arg97 (−12.91), Tyr104 (−6.98), Arg105 (−4.96) |
| ClusPro | 3, 4 | −91.38 | Phe633 (−7.47), Asp345 (−4.67), Ser402 (−4.05) | Arg97 (−6.48), Arg105 (−5.48), Thr26 (−4.82) |
| ClusPro | 7, 8 | −74.14 | Gln349 (−8.25), Phe576 (−6.49), Tyr636 (−4.47) | Arg97 (−6.97), Met50 (−6.27), Thr26 (−5.74) |
| ZDOCK | 2* | −69.66 | Phe634 (−4.55), Phe633 (−4.52), Thr635 (−4.06) | Arg97 (−7.30), Tyr104 (−5.56), Val108 (−2.68) |
| HDOCK | 3, 4 | −55.21 | Phe634 (−3.78), Ser312 (−3.74), Thr635 (−3.73) | Arg105 (−6.52), Arg97 (−4.71), Thr26 (−3.10) |
| ZDOCK | 1* | −51.83 | Ile313 (−4.13), Asp632 (−3.95), Glu642 (−3.63) | Arg97 (−12.7), Lys31 (−5.74), Arg105 (−4.11) |
| ZDOCK | 3,4 | −42.97 | Phe634 (−5.34), Gln346 (−3.34), Asp632 (−3.30) | Arg105 (−8.06), Arg97 (−6.78), Lys31 (−3.76) |
| pyDock | 7* | −25.78 | Phe633 (−5.10), Phe634 (−4.08), Tyr636 (−3.58) | Arg29 (−5.32), Arg105 (−2.75), Leu27 (−2.62) |
*
Single docking pose, missing a similar symmetric pose bound to the other monomers of the homodimeric structure of PADI4.