All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
The reviewer is completely satisfied by your revision, and the amended manuscript is acceptable now..
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
This is a well-written manuscript. The conclusion is backed by simulation data and analyses.
The method section has been revised by the authors following the suggestion. The result can be reproduced following the protocol.
No comments
The authors have addressed all my queries and modified the manuscript accordingly. However, I still believe that a multiple copy simulation would be beneficial for dynamic study.
Please address critiques of the reviewers, paying special attention to the comments of reviewer #2.
[# PeerJ Staff Note: Please ensure that all review comments are addressed in a rebuttal letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the rebuttal letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
The article is well written.
I have issues with the originality of this work. This is essentially an incremental piece of work. It does not provide a substantial advance on the area described and neither does it have conceptual novelty
I have issues with the originality of this work. This is essentially an incremental piece of work. It does not provide a substantial advance on the area described and neither does it have conceptual novelty
The authors are recommended to have a thorough relook at this manuscript and significantly improve.
No comments
No comments
1. The 80 ns simulation time used in this study is too short of ensuring convergence. The authors have not provided the time evolution of RMSD also. Longer simulations and/or multiple copy simulations will be a better choice.
2. How the 150-loop dynamics affect the drug binding mechanisms of NA should be discussed clearly.
3. It would be helpful to show how the pocket cavity volume affects the OTV binding.
4. The disulfide bonds are essential for NA structure, and they must be careful about that, which is not clear from the methods section.
5. The binding free energies calculated with MMPBSA are shown to be very sensitive to many factors, such as the value of the dielectric constant chosen for the protein or the conformational entropy (which can be improved by running multiple replicates). The values calculated here must be interpreted very carefully.
6. The MMPBSA calculation provides the other energetic components (like vdW, Elect, Pol-sol, and non-pon-sol) in Table 1.
7. The role of molecular water in OTV recognition is missing in this text, as they play an important role in inhibitor binding.
8. A representative structure that summarizes the analysis in sections 2.1 and 2.2 would be beneficial.
No comment
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.