PONE-D-24-20487Molecular Dynamics Simulation based Prediction of T-cell Epitopes for the Production of Effector Molecules for Liver cancer immunotherapyPLOS ONE

Dear Dr. Muhammad,

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Sheikh Arslan Sehgal, PhD

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: N/A

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

Reviewer #2: No

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: 1.In the materials and methods section, the authors should put the access link in front of the names of the software, servers, and databases.

2.The authors should explain why they set the antigenicity threshold to 0.5 in the manuscript. Do they have a reference for this value?

3.Please calculate and report the aliphatic index and GRAVY parameters of the vaccine construct.

4.The authors should perform disulfide engineering of the vaccine construct.

5.Please compare the characteristics of the vaccines designed in this study with the vaccines designed in other authors' studies. For this, please use the following references and cite them.

https://doi.org/10.3390/vaccines11020263

https://doi.org/10.2174/1573409919666230612125440

https://doi.org/10.1080/07391102.2023.2258403

https://doi.org/10.1016/j.ijbiomac.2024.131517

https://doi.org/10.1007/s12033-023-00949-y

Reviewer #2: The manuscript is a bioinformatic analysis of TSA and TAA for Liver cancer. Although the immunoinformatic analysis, molecular dynamics analysis, immune simulation studies are also sufficient to predict the usage of this epitope based vaccine but unless it is validated by using cancer cell lines or patients cells, the results cannot be confirmed. Animal model studies with immunogenic response and tumour regression is required to further validate their claim. So many such vaccine candidates are predicted for almost all the diseases and cancers speacially in COVID times and are stll being predicted, but they need to be validater preclinically or experimentally.

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Reviewer #1: No

Reviewer #2: Yes: Sadhna Sharma

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Molecular Dynamics Simulation based Prediction of T-cell Epitopes for the Production of Effector Molecules for Liver cancer immunotherapy

PONE-D-24-20487R1

Dear Dr. Muhammad,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Sheikh Arslan Sehgal, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: -Dear authors, I would like to thank you for carefully considering all the comments. I hope that this manuscript can have a great impact on liver cancer immunotherapy after its final acceptance.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

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