Saturday, June 1, 2013

PLoS ONE rejects, we appeal ... and loose

Original reviews
Our rebuttal
The rejection
Our appeal
Sent: Wednesday, May 29, 2013 9:51 PM
To: Jan Halborg Jensen
Subject: PLOS ONE Decision: PONE-D-13-07851R2

In Silico Screening of 393 Mutants Facilitates Enzyme Engineering of Amidase Activity in CalB

Dear Dr. Jensen,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript does not meet our criteria for publication and must therefore be rejected.


The resubmitted manuscript has been assigned to two Academic Editors who have read the paper carefully. In addition we obtained one further review which also requested major revision.

One of the concerns outlined by the previous reviewers was that no real revision was offered in response to their (in places very reasonable) comments. My co-editor and I agree that the major issue with the paper is that is that it does not meet the journal's Criterion 3 for publication: "Experiments, statistics, and other analyses are performed to a high technical standard and are described in sufficient detail". While we do not share some of the concerns over the methodology that were raised by the original reviewers, we do feel that paper does not describe the work well enough. Reading the manuscript independently my coeditor and I both formed the opinion that the paper was confusing and in many places unclear (in my case even when read in conjunction with reference 1). For this reason we uphold the decision to reject this paper.

I am sorry that we cannot be more positive on this occasion, but hope that you appreciate the reasons for this decision.

Yours sincerely,

xxx & xxx
Academic Editors

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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 this form and submit your "Accept" recommendation.

Reviewer #4: (No Response)

Please explain (optional).

Reviewer #4: (No Response)

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 #4: Partly

Please explain (optional).

Reviewer #4: It is not clear how the protein variants are characterized once they are purified. What concentration of enzyme is used? Is the protein folded (did they measure structure using CD or some other spectroscopic indicator)? Is the protein intact - no proteolysis or degradation during expression or purification (i.e. using mass spectrometry, sds page, or HPLC). Experimental methods need to be expanded to include how sample quality was assured.

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

Reviewer #4: No

Please explain (optional).

Reviewer #4: Choosing a cutoff for post-hoc analysis that maximizes the correlation between experimental outcome and computational prediction is not an acceptable way to validate a computational method. With the small sample size, is 15/22 a better outcome than 11/22 (i.e. 50% random correlation)? A p-value or t-test is needed.

A more quantitative comparison of the reaction energy barrier and the degree of activity enhancement / reduction needs to be performed. This is more meaningful than classifying the outcomes into two categories.

4. Does the manuscript adhere to standards in this field for data availability?

Authors must follow field-specific standards for data deposition in publicly available resources and should include accession numbers in the manuscript when relevant. The manuscript should explain what steps have been taken to make data available, particularly in cases where the data cannot be publicly deposited.

Reviewer #4: Yes

Please explain (optional).

Reviewer #4: (No Response)

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 below.

Reviewer #4: Yes

6. Additional Comments to the Author (optional)

Please offer any additional comments here, including concerns about dual publication or research or publication ethics.

Reviewer #4: (No Response)

7. If you would like your identity to be revealed to the authors, please include your name here (optional).

Your name and review will not be published with the manuscript.

Reviewer #4: (No Response)

[NOTE: If reviewer comments were submitted as an attachment file, they will be accessible only via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.]

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For journal use only: PONEDEC3

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