Dear Dr Lercher,

Thank you for submitting your manuscript entitled "A general prediction model for substrates of transport proteins" for consideration as a Research Article by PLOS Biology.

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Suzanne

Suzanne De Bruijn, PhD,

Associate Editor

PLOS Biology

sbruijn@plos.org

Dear Dr Lercher,

Thank you for your patience while we considered your revised manuscript "A general prediction model for substrates of transport proteins" for publication as a Methods and Resources Article at PLOS Biology. Please accept my apologies for the delays that you have experienced during this round of the peer review process. This revised version of your manuscript has been evaluated by the PLOS Biology editors, the Academic Editor and two of the original reviewers.

Based on the reviews, I am pleased to say that we are likely to accept this manuscript for publication, provided you satisfactorily address the following editorial and data-related requests that I have provided below (A-E):

(A) We would like to suggest the following modification to the title:

“SPOT: a machine learning model that predicts specific substrates for transport proteins”

(B) You may be aware of the PLOS Data Policy, which requires that all data be made available without restriction: http://journals.plos.org/plosbiology/s/data-availability. For more information, please also see this editorial: http://dx.doi.org/10.1371/journal.pbio.1001797

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Figure 2A-B, 3A-B, 4A-B, 5A-B, S1-6

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As you address these items, please take this last chance to review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the cover letter that accompanies your revised manuscript.

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Best wishes,

Richard

Richard Hodge, PhD

Senior Editor, PLOS Biology

rhodge@plos.org

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Reviewer remarks:

Reviewer #2: The authors have submitted a revision that is highly responsive to the previous concerns raised, not only by myself but also the other two reviewers. All issues have been addressed in a thoughtful and rigorous manner, and various additional analyses have been added that further strengthen this study. I have no further comments.

Reviewer #3: The authors have appropriately replied to my points, and have apparently fixed the problem with entered KEGG id's.

I ran the following 4 more tests for recently discovered transport functionalities:

https://elifesciences.org/articles/92615

reported in April 2024 that D-serine is a substrate of human SLC5A8 (SMCT1) and SLC7A10 (Asc-1).

(1) I tested Spot with SLC5A8 and C00740: this gave a prediction score of 0.050 which is incorrect.

(2) Then I tested Spot with SLC7A10 and C00740: this gave a prediction score of 0.68 which is correct.

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PMID: 38507452 reported in March 2024 that the orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing Protein 1 (MFSD1)

transports lysine/arginine/histidine-containing dipeptides, e.g. the dipeptide KP

(3) I tested Spot with Mfsd1 and the Inchi-String of Lysyl-proline:InChI=1S/C11H21N3O3/c12-6-2-1-4-8(13)10(15)14-7-3-5-9(14)11(16)17/h8-9H,1-7,12-13H2,(H,16,17)/p+1

this gave a prediction score of 0.12 which is incorrect

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https://www.biorxiv.org/content/10.1101/2024.03.22.586268v1.full.pdf

reports that VC0430 from Vibrio cholerae is a monomeric high affinity Transporter for L-glutamate.

(4) I used the sequence https://www.ncbi.nlm.nih.gov/protein/AAF93603.1

that appears to belong to VC0430 and the KEGG ID of l-Glutamate: C00025

I gave this to Spot. This gave a prediction score of 0.60 which is correct.

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I believe that the authors of Spot overall did a very good job. The tool seems to work surprisingly well for compounds and transporters that are reasonably well represented by their training data set. My 4 new tests show that transferability to orphan transporters and new transport scenarios gave mixed results. Also, my previous tests only were successful for 4 out of 6 cases. Thus, users of Spot who want to discover truly novel substrates may experience that the reported 92% accuracy does not extend into such areas.

But I still think Spot is a good and useful addition to the literature and I am supportive of acceptance.

Dear Dr Lercher,

On behalf of my colleagues and the Academic Editor, Raimund Dutzler, I am pleased to say that we can accept your manuscript for publication, provided you address any remaining formatting and reporting issues. These will be detailed in an email you should receive within 2-3 business days from our colleagues in the journal operations team; no action is required from you until then. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed any requested changes.

Please take a minute to log into Editorial Manager at http://www.editorialmanager.com/pbiology/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

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Thank you again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study. 

Best wishes,

Richard 

Richard Hodge, PhD

Senior Editor, PLOS Biology

rhodge@plos.org

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