However, as strong distance and contact restraints have been implemented in the second-round simulation, the topology improvement of the models is modest.
The latest second-round simulations show Ms Rousseff and Ms Silva running neck and neck.For a while it looked as if Ms Silva would carry the run-off with ease.
(Ms Rousseff retains a comfortable 18-point lead; she also beats both pretenders in second-round simulations).Related topics Latin American politics Brazil Brazilian politics World politics Elections and votingThis is only the latest twist in a campaign that has had more of them than a Brazilian telenovela.
Ms Rousseff, who in August trailed Ms Silva by as much as ten points in second-round simulations, now enjoys a healthy lead over either challenger, thanks to ample media exposure that has allowed her to play up successes and bash rivals.
A similar plot was also obtained from the average conformation of Cluster 3 of the second-round simulations (Figure 5).
These results suggest that the average or representative conformation in Cluster 3 of the second-round simulations best represents the AHPBoNTAe complex structure in water.
The numbers of the inhibitor conformations in Clusters 1 5 of the second-round simulations are 459, 201, 2762, 178, and 400, respectively.
The same cluster analyses of the second-round simulations identified again one cluster of the BoNTAe conformations and five clusters of the AHP conformations.
Consistently, the average conformation of AHPBoNTAe in Cluster 3 of the second-round simulations has a C&F RMSD of 0.85 Å.
Interestingly, the most populated inhibitor conformation (Cluster 3) of the second-round simulations is nearly identical to the third most popular inhibitor conformation (Cluster 2) of the first-round.
However, the most popular inhibitor conformation (Cluster 1) of the first-round simulations disappeared in the second-round, suggesting that AHP adopts only one conformation in the BoNTAe active site.
