PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences

Bulat Faezov; Roland L. Dunbrack Jr.

doi:10.1371/journal.pone.0253411

Peer Review History

Original SubmissionMay 5, 2021
28 May 2021 Decision Letter - Yang Zhang, Editor PONE-D-21-14953 PDBrenum: a webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences PLOS ONE Dear Dr. Dunbrack Jr., Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jul 08 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes ****** 3. 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The paper describes PDBrenum, a python tool and webserver to renumber residues according to Uniprot in mmCIF or PDB files. This paper address a significant problem, as the authors show that ~38% of PDB contains proteins that are not numbered according to Uniprot. The code is available on github and the webserver is online and working. I have some minor concerns to make the manuscript better. - Figures 1, 5 and 6 in the pdf have a low resolution and are hard to read. - In figure 4, there is a mismatch between the picture and its description. Example: "comp_uni" and "human_uni" do not appear in the picture. - What happens to mutated residues? Are they kept in the file or replaced by the ones of the wild type protein in Uniprot? Is the numbering scheme for them corrected? Maybe the authors could comment about it in the manuscript. Reviewer #2: The authors provide a renumbering tool for PDB files, which can be used on-line or as a standalone program. The tool will renumber following UniProt numbering, hence numbering over multiple PDB structures of the same protein will be consistent. This will prove to be or become a most valuable tool. I have two comments: - after cloning the git, conda is used to set up the proper environment. This is not necessary if the environment is already suited for use of PDBrenum (correct python, etc). conda is not always distributed as an easy to install package on linux distributions. A note should be added that for use of standalone PDBrenum, and in absence of conda, the following packages with versions blabla should be installed. - the images were of extremely low resolution. so low that I could hardly read figure 1, let alone the figure with the green lines indicating was had been changed. ****** 6. 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: Yes:** Ariane Nunes Alves Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible 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.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. 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Revision 1
3 Jun 2021 Author Response Dear Dr. Zhang, We thank the editor and the reviewers for their helpful comments. We have revised the manuscript in response to the reviewers’ concerns as detailed below. Best wishes, Bulat Faezov Roland Dunbrack (Responses to reviewers’ comments are prefixed with “”). Reviewer #1: The paper describes PDBrenum, a python tool and webserver to renumber residues according to Uniprot in mmCIF or PDB files. This paper address a significant problem, as the authors show that ~38% of PDB contains proteins that are not numbered according to Uniprot. The code is available on github and the webserver is online and working. I have some minor concerns to make the manuscript better. - Figures 1, 5 and 6 in the pdf have a low resolution and are hard to read. In the PDF, PLOS ONE provided a much lower resolution of the figures than we submitted and at the top of each page with a figure there is a link to the submitted tif files that the reviewer can click to get the higher resolution figures. In any case, we have created even higher resolution versions of the screenshot figures by using a higher-resolution monitor. Please use the links at the top of each figure page to evaluate the resolution. - In figure 4, there is a mismatch between the picture and its description. Example: "comp_uni" and "human_uni" do not appear in the picture. Thank you for pointing this out. The caption was written for a previous version of the log file and has now been corrected. - What happens to mutated residues? Are they kept in the file or replaced by the ones of the wild type protein in Uniprot? Is the numbering scheme for them corrected? Maybe the authors could comment about it in the manuscript. Mutated residues are kept with the residue types in the original PDB or mmCIF files. SIFTS annotates mutations that do not match the UniProt residue type. The following sentence was added to the paper: Mutations in a UniProt sequence in a PDB entry are annotated in SIFTS files, and the mutated residue type and residue number are retained within the output mmCIF or PDB files Reviewer #2: The authors provide a renumbering tool for PDB files, which can be used on-line or as a standalone program. The tool will renumber following UniProt numbering, hence numbering over multiple PDB structures of the same protein will be consistent. This will prove to be or become a most valuable tool. I have two comments: - after cloning the git, conda is used to set up the proper environment. This is not necessary if the environment is already suited for use of PDBrenum (correct python, etc). conda is not always distributed as an easy to install package on linux distributions. A note should be added that for use of standalone PDBrenum, and in absence of conda, the following packages with versions blabla should be installed. We have added a statement to the README.md file that tells the user that PDBrenum may work outside of a conda environment if biopython, pandas, numpy, tqdm, ipython, lxml, and requests are all installed. The user can try PDBrenum and if no error is returned, then it works with the versions of these packages that the user already has. The user can also install the versions of these packages listed in the README file one by one. Also, wget and curl commands can be used to download files programmatically from the webserver if there are any problems with the python version. We added the following to the paper also: If the Python packages listed above are already installed (or similar versions of them), then PDBrenum may work outside of a conda environment. The user can try it that way, and if no errors are returned, then the program works. - the images were of extremely low resolution. so low that I could hardly read figure 1, let alone the figure with the green lines indicating was had been changed. In the PDF, PLOS ONE provided a much lower resolution of the figures than we submitted and at the top of each page with a figure there is a link to the submitted tif files that the reviewer can click to get the higher resolution figures. In any case, we have created even higher resolution versions of the screenshot figures by using a higher-resolution monitor. Please use the links at the top of each figure page to evaluate the resolution. https://doi.org/10.1371/journal.pone.0253411.r002
7 Jun 2021 Decision Letter - Yang Zhang, Editor PDBrenum: a webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences PONE-D-21-14953R1 Dear Dr. Dunbrack Jr., 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Yang Zhang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0253411.r003
Formally Accepted
25 Jun 2021 Acceptance Letter - Yang Zhang, Editor PONE-D-21-14953R1 PDBrenum: a webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences Dear Dr. Dunbrack Jr.: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Yang Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0253411.r004

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