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The manuscript has been significantly improved by the authors and now can be accepted in its current form.
[# PeerJ Staff Note - this decision was reviewed and approved by Gwyn Gould, a PeerJ Section Editor covering this Section #]
Authors addressed all of my comments. The revised manuscript can be accepted for final publication.
Authors addressed all of my comments. The revised manuscript can be accepted for final publication.
Authors addressed all of my comments. The revised manuscript can be accepted for final publication.
Authors addressed all of my comments. The revised manuscript can be accepted for final publication.
The manuscript meets the standards of the journal. No comments.
No comments
No comments
The authors have made satisfactory changes to the manuscript in response to the reviews.
Its of acceptable quality
Experiments are designed systematically.
Results are validated.
The revised version of manuscript entitled “Virtual screening of flavonoids as potential RIPK1 inhibitors for neurodegeneration therapy” is significantly improved than previous version. Authors have successfully addressed all of my queries and manuscript is appealing for publication. Therefore, I recommend acceptance of manuscript.
Experts in the field have carefully reviewed your manuscript and have raised a number of serious concerns that preclude its acceptance in the present form. This paper has been recommended for MAJOR REVISIONS. I invite you to respond to the reviewers' comments and revise your paper accordingly. The revised version will be re-evaluated by the original reviewers or in some circumstances by new reviewers.
**PeerJ Staff Note:** It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors are in agreement that they are relevant and useful.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
1. Are there controversies in this field? What are the most recent and important achievements in the field? In my opinion, answers to these questions should be emphasized. Perhaps, in some cases, novelty of the recent achievements should be highlighted by indicating the year of publication in the text of the manuscript.
2. The results and discussion section is very weak and no emphasis is given on the discussion of the results like why certain effects are coming in to existence and what could be the possible reason behind them?
3. Conclusion: not properly written.
4. Results and conclusion: The section devoted to the explanation of the results suffers from the same problems revealed so far. Your storyline in the results section (and conclusion) is hard to follow. Moreover, the conclusions reached are really far from what one can infer from the empirical results.
5. The discussion should be rather organized around arguments avoiding simply describing details without providing much meaning. A real discussion should also link the findings of the study to theory and/or literature.
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The manuscript satisfies all criteria. No comments.
The manuscript satisfies all criteria. No comments.
The manuscript satisfies all criteria. No comments.
This is a well written paper with useful results. The discussion could have used a little more detail about the experimental outcomes and future experiments.
The authors have explained the results and validation in detail.
The study is designed systematically.
The manuscript entitled “Virtual screening of flavonoids as potential RIPK1 inhibitors for neurodegeneration therapy” by Bepari and co-authors reported three flavonoids as a potential RIPK1 inhibitor. Authors have screened 4858 flavonoids at the kinase domain of RIPK1 using AutoDock Vina. Furthermore, authors employed MD simulation to assess the stability of protein-ligand complex during dynamics environment. Moreover, authors did MMPBSA to explore the energetic stability of protein-ligand complex. The manuscript is written well, and the work is performed systematically. However, I have queries and suggestions that need to be addressed prior to consideration of manuscript. I recommend a major revision and here are my comments for the manuscript:-
1. In MD analysis Figures (Figure 3, 6, and 7), authors should compare RMSD, RMSF, and Rg results in a same graph. Authors can refer following articles for graph modifications:- (https://doi.org/10.1016/j.molstruc.2022.132476; https://doi.org/10.1080/07391102.2021.1936179)
**PeerJ Staff Note:** It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors are in agreement that they are relevant and useful.
2. Authors have performed MMPBSA to evaluate the energetic stability of niti, Pino, and Para bound complexes. Authors should perform amino acid residues decomposition analysis to check the contributions of important amino acid residues to stabilized protein-ligand complex. Authors can refer following articles for amino acid residues decomposition analysis:- (https://doi.org/10.1016/j.molstruc.2022.132476; https://doi.org/10.1080/07391102.2021.1936179)
**PeerJ Staff Note:** It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors are in agreement that they are relevant and useful.
3. There are several typos and grammatical mistakes. So, authors need to thoroughly screen manuscript to fix typos and grammatical errors.
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