Er two docking Aifm aromatase Inhibitors targets applications didn’t incorporate energy minimization procedures. The PatchDock’ model was probably the most perturbed, as when compared with the outcome of the docking routine, due to the manual editing, which may possibly explain the pronounced effect of energy minimization. 24) I never consider 45 ns is usually a extended adequate simulation to say anything about stability with the complete complicated, particularly given the huge size of this complex. 25) “.. Hence, MD simulations revealed only 1 model (the PatchDock’ model, Fig. 1) that kept the proper domain architecture and intact geometry throughout the MD simulation..” this worries me. Could it be that a considerably more careful equilibration of MD is required Or that the complexes are wrong Authors’ response: As we’ve explicitly emphasized inside the revised manuscript, the model structures could be all wrong, they’re just theoretical predictions that await experimental scrutiny. Our task was, nonetheless, to determine the residues of Apaf-1 which might be involved in binding of cytochrome c. We think that we have solved this issue by combining structural modeling with sequence analysis. We had to limit our MD simulation time to 45 ns because of the substantial size of your system. Nonetheless, we assume thatthe simulation time was enough to discriminate a mechanically “wrong” structure from a stable 1. The heat maps in Extra file 1: Figure S1 show that while the stability on the ClusPro structure decreased with time, the stability of your PatchDock’ structure enhanced via the MD simulation. So it seems unlikely that the PatchDoc’ structure would break up upon a longer MD simulation. 26) “..of Apaf-1 is much more or much less evenly negatively charged..” more or less Deleted 27) “..correlation coefficient of 0.9463 as in comparison to 0.9558..” how calculated Authors’ response: We’ve used UCSF Chimera package [84]. The reference to this software program has been added for the Solutions section. 28) Error: “.. Electrostaticpolar interactions or bonds that contain salt bridges and possible H-bonds are commonly regarded as inside a 4 cutoff..” the 4A cutoff is for H-bonds. Salt bridges have a tendency to have a cutoff of 8-12A or perhaps longer. The shorter salt bridges sometimes are known as H-bonded salt bridges. This also why there ought to be at the very least 12A in between the solute along with the simulation box… Authors’ response: We don’t see an error right here. The criterion for identifying a salt bridge, as initially proposed by Barlow and Thornton [54], is the fact that the distance involving the heavy atoms of the ionizable groups of charged residues needs to be much less than four This HQNO Epigenetic Reader Domain cut-off of four has been utilized for defining salt bridges in numerous research, see [503] and references therein, too as within the prior research of cytochrome c interactions with its partners [42]. The cut-off of 4 was also taken for salt bridges inside the paper of de Groot and co-workers [49] that was co-authored by the Reviewer. We’ve added the references to all these classical papers towards the revised manuscript. It really is essential to note that we also talk about the long-range interactions. In the original manuscript, we have deemed a cut-off of five as experimental studies show detectable interactions even at this distance [55], additionally towards the 3 cut-off employed to identify robust hydrogen bonds (Table 3 inside the revised manuscript). To address this comment with the Reviewer, within the revised manuscript, we have added the information that had been collected having a cut-off of 6 to illustrate that any additional enhance within the cut-offShalae.
