Peer Review History

Original SubmissionNovember 20, 2019
Decision Letter - Charlotte M Deane, Editor, Arne Elofsson, Editor

Dear Dr Duarte,

Thank you very much for submitting your manuscript "Preparing for the 3D data deluge: real time structural search at the scale of the PDB and beyond" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

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Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Charlotte M Deane

Associate Editor

PLOS Computational Biology

Arne Elofsson

Deputy Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Review comments attached as pdf. Predominantly, what is needed is the clarification of the method through the use of non-ambiguous language.

Reviewer #2: The authors present an approach for fast retrieval of similar structures from PDB, using 3D Zernike moments. The proposed approach is an improvement over existing tools and the speed of the method is a big advantage and shows better performance in authors benchmark. The implementation seems robust and is a useful tool for the community. I have a few minor points that will help with user interpretation of results.

1) How does the approach perform (and rank) in case of partial alignments where only part of the larger protein is matched?

2) What are the safe thresholds of the total score to find close and distantly related structures? How much does Zernike descriptors contribute to the total score in general? A discussion would help users.

3) The method can deal with EM volumes but the current implementation and tests doesn’t include these. It is useful to discuss this although I noted that this is mentioned as part of future developments.

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Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: No: The approach used for generating the dataset is included but seemingly not the list of structures that resulted. list/spreadsheet of optimised zernike/geometric distance metric weights could also be included.

Reviewer #2: No: The benchmark datasets used for tests

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Reviewer #1: No

Reviewer #2: No

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Attachments
Attachment
Submitted filename: reviewer-comments.pdf
Revision 1

Attachments
Attachment
Submitted filename: BioZernike review - PLoS CB.pdf
Decision Letter - Charlotte M Deane, Editor, Arne Elofsson, Editor

Dear Dr Duarte,

We are pleased to inform you that your manuscript 'Real time structural search of the Protein Data Bank' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Charlotte M Deane

Associate Editor

PLOS Computational Biology

Arne Elofsson

Deputy Editor

PLOS Computational Biology

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Formally Accepted
Acceptance Letter - Charlotte M Deane, Editor, Arne Elofsson, Editor

PCOMPBIOL-D-19-01993R1

Real time structural search of the Protein Data Bank

Dear Dr Duarte,

I am pleased to inform you that your manuscript has been formally accepted for publication in PLOS Computational Biology. Your manuscript is now with our production department and you will be notified of the publication date in due course.

The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript.

Soon after your final files are uploaded, unless you have opted out, the early version of your manuscript will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers.

Thank you again for supporting PLOS Computational Biology and open-access publishing. We are looking forward to publishing your work!

With kind regards,

Laura Mallard

PLOS Computational Biology | Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom ploscompbiol@plos.org | Phone +44 (0) 1223-442824 | ploscompbiol.org | @PLOSCompBiol

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