Information for Authors

Scope of the Journal

Protein Engineering, Design and Selection (PEDS) publishes high-quality research papers and review articles relevant to the engineering, design and selection of proteins for use in biotechnology and therapy, and for understanding the fundamental link between protein sequence, structure, dynamics, function, and evolution. With reputable protein scientists as editors and board members, PEDS offers expert, high-quality peer review and a fast turnaround time.

Editorial Policies 
Submissions 
Production 

Ethical Policies

Authors should observe high standards with respect to publication ethics as set out by the Commission on Publication Ethics (COPE). Cases of ethical misconduct will be dealt with in accordance with the COPE guidelines.

Further information about OUP’s ethical policies.

Authorship

Authorship is confined to those who have made a significant contribution to the design and execution of the work described. Any contributors whose participation does not meet the criteria for authorship should be acknowledged but not listed as an author. For a detailed definition of authorship, please see the International Committee of Medical Journal Editors (ICMJE) definitions of authors and contributors. 

The Journal does not allow ghost authorship, where an unnamed author prepares the article with no credit, or guest/gift authorship, where an author who made little or no contribution is listed as an author. The Journal follows Committee on Publication Ethics (COPE) guidance on investigating and resolving these cases. For more information, please see the OUP Publication Ethics page. 

After manuscript submission, no authorship changes (including the authorship list, author order, and who is designated as the corresponding author) should be made without the approval of the editor. All co-authors must agree on the change(s), and neither the Journal nor the publisher mediates such disputes. If individuals cannot agree on the authorship of a submitted manuscript, contact the editorial office. The dispute must be resolved among the individuals and their institution(s) before the manuscript can be accepted for publication. If an authorship dispute or change arises after a paper is accepted, contact OUP’s Author Support team. COPE provides guidance for authors on resolving authorship disputes. 

CRediT  

The Journal uses the contributor roles taxonomy (CRediT), which allows authors to describe the contributor roles in a standardized, transparent, and accurate way. Authors should choose from the contributor roles outlined on the CRediT website and supply this information upon submission. You may choose multiple contributor roles per author. Any other individuals who do not meet authorship criteria and made less substantive contributions should be listed in your manuscript as non-author contributors with their contributions clearly described.

Peer Review

All papers accepted for publication will have undergone a high standard of peer reviewed by experts in the relevant field. Typically, new submissions are initially reviewed by the Editor-in-Chief and his Associates. At this stage manuscripts may be rejected without peer review if it is felt that they are not of high enough priority or not relevant to the journal. This means that you are given a quicker decision and do not need to wait for a full review to be completed.

If the editors think a paper may be worth publishing, they will send it out to two or more independent reviewers to provide feedback on the quality of the work. This journal adheres to a single-anonymised review policy in which the authors’ identities are revealed to reviewers, but the reviewers’ identities are kept confidential. Authors are required to respond to all reviewer comments when submitting revised copies of their manuscript. Rebuttal of reviewer comments should be directed by the author to the Editor.

You may find more details on the peer review process page.

Data Policy

The journal encourages all authors, where ethically possible, to publicly release all data underlying any published paper. We suggest that data be presented in the manuscript's supporting files, or deposited in a public repository whenever possible. In addition, excerpts from the data may be included in the main article for illustrative purposes if desired. Accession codes for protein structural data (Protein Data Bank, Biological Magnetic Resonance Data Bank ) must be provided. Authors are also encouraged to deposit functional data on Protabank, the protein engineering database, and provide accession codes.

ORCID

Protein Engineering, Design and Selection (PEDS) requires submitting authors to provide an ORCID iD at submission to the journal. More information on ORCID and the benefits of using an ORCID iD is available. If you do not already have an ORCID iD, you can register for free via the ORCID website.

Preprint Policy

Authors retain the right to make an Author’s Original Version (preprint) available through various channels, and this does not prevent submission to the journal. For further information see our Online Licensing, Copyright and Permissions policies. If accepted, the authors are required to update the status of any preprint, including your published paper’s DOI, as described on our Author Self-Archiving policy page.

Self-Archiving Policy

You may self-archive versions of your work on your own webpages, on institutional webpages, and in other repositories. If you want more information about the reuse rights you retain if you publish with us, please visit our Author Self-Archiving Policy page.

Conflict of Interest

When submitting a paper, you and your co-authors must declare any potential conflicts of interest. You must do this by including a Conflict of Interest statement in your submitted manuscript or by providing the relevant details on our online submission site and by including a Conflict of Interest statement in your submitted manuscript.

You can find a detailed definition on the conflicts of interest page.

Submissions

Manuscripts can be submitted in any common document format that can be easily opened and read by others. A single PDF or Word file is usually reliable. At first submission, it is not necessary to apply formatting to match house style. Instead, simply ask: would I enjoy reading and reviewing a manuscript formatted in this way?

We will consider your manuscript as long as

• it is your own original work and does not duplicate any previously published work, including your own;
• it is not under consideration, in peer review, or accepted for publication in any journal other than Protein Engineering, Design, and Selection
• it has not been published in any other journal; and
• it contains nothing abusive, defamatory, libelous, obscene, fraudulent, or illegal.

Authors should observe high ethical standards and obey publication best practices. The following are all unacceptable:

• data falsification or fabrication
• plagiarism, including duplicate publication of your own work without proper citation
• misappropriation of work

We treat any case of ethical or publication malpractice very seriously. We will address them in accordance with the Committee on Publication Ethics (COPE) guidelines. Visit OUP’s ethical policies guidelines for further information.

How to Submit

You must submit your paper via our web-based submission system, which may be found on the journal's ScholarOne Manuscripts page. If you have not published with Protein Engineering, Design, and Selection before, you will need to create an account. Visit the ScholarOne FAQs page for more information. Questions about submitting can be sent to the editorial office at [email protected].

You must also submit a statement that your paper has not been published elsewhere and has not been simultaneously submitted for publication elsewhere.

Article Type

This journal publishes several different article types, as described below. While we provide word, reference, and table/figure counts as suggestions, we are happy to review and publish articles that deviate from this preferred format.  

Original Articles—Suggested Maximum Word Count: 4,000 (not including abstract, methods, references, and figure legends)

• abstract—suggested maximum word count: 150
• references— suggested maximum references: 50
• tables and figures— suggested maximum of 6 display items total

Each submission must contain the following sections: introduction, methods, results, discussion, and acknowledgements. The Results and Methods sections should be subdivided into topical sections by using short headers.

Short Communications—Suggested Maximum Word Count: 2,500 (not including abstract, references, and figure legends)

• abstract—suggested maximum word count: 100
• references—suggested maximum references: 30
• tables and figures—suggested maximum of 4 display items total

Short communications comprise announcements of new and focused research findings, useful computer software, along with a description of relevant applications and internet usage, and the announcement of novel protocols. Authors have the opportunity to present their work in the same format as an original research article, or may combine methods, results and discussion in a single section.

Review Articles—Suggested Maximum Word Count: 4,000 (not including abstract, references, and figure legends)

• abstract—suggested maximum word count: 150
• references—suggested maximum references: 50
• tables and figures—suggested maximum of 4 display items total

Reviews should inform readers of the state-of-the-art of a particular area, provide a critical view, or a historical perspective. They should be comprehensive, critical, and balanced. Although the focus may be the author's own work, references to the works of others should be included.

Third-Party Permissions

If you wish to reproduce any material for which you do not own the copyright—including quotations, tables, or images—you must obtain permission from the copyright holder. The permissions agreement must include the following documents:

• nonexclusive rights to reproduce the material in your article in Protein Engineering, Design and Selection
• electronic rights, preferably for use in any form or medium
• lifetime rights to use the material
• worldwide English-language rights

Further information is available on the permissions page.

Manuscript Preparation: Format, Structure, and Style

Presubmission Language Editing

If you are not confident in the quality of your English, you may wish to use a language-editing service to ensure that editors and reviewers understand your paper. Language editing is optional and does not guarantee that your manuscript will be accepted. Edited manuscripts will still undergo peer review by the journal.

Title Page

Please include the following:

• the title of your paper (15 words or less)
• all author names and affiliations
• email address of one corresponding author

Abstract

Abstracts have a maximum length of 150 words and must not contain reference citations or abbreviations.

Style

After initial review, you may be asked to supply editable files that match journal formatting requirements, and high-resolution figures.

The journal follows the author-date reference style. More information on the referencing style can be found in the journal mini-style checklist. Please ensure that you refer to these requirements when preparing your manuscript.

More information is available.

If you use EndNote to facilitate referencing citations (not required for submission), this journal's style is available for use on the EndNote website.

Abbreviations

Please define nonstandard abbreviations at the first occurrence.

Tables

You must number all tables (e.g., Table 1, Table 2, Table 3) and reference them in the text. You must place all tables at the end of the main text. Tables should be in an editable format, and not embedded as an image file.

References

You may format references in any readable style at submission. You are responsible for the accuracy of reference information. Later, authors may be asked to comply with the journal's citation convention.

Acknowledgments and Funding

Acknowledgments and funding information should be included at the end of your manuscript. Please fully cite any relevant funding information, including specific grant numbers.

LaTeX

Information on LaTeX files and formatting is available. The LaTex template is available here.

Figures

You must include figure titles and legends within the manuscript file—they should not be included in the image file.

You must submit each figure as an individual image file. Submit all panels of a multipanel figure on a single page as one file. For example, if the figure has 3 panels, the figure should be submitted as one file. Each panel should be labelled as a letter (a, b, c, d, etc.) in the upper-left corner of each panel.

Images of photographs or paintings can be provided as raster images. Common examples of raster images are .tif/.tiff, .raw, .gif, and .bmp file types. The resolution of raster files is measured by the number of dots or pixels in a given area, referred to as “dpi” or “ppi.”

• minimum resolution for electronic images (i.e., for on-screen viewing): 72dpi

Images of maps, charts, graphs, and diagrams are best rendered digitally as geometric forms called vector graphics. Common file types are .eps, .ai, and .pdf. Vector images use mathematical relationships between points and the lines connecting them to describe an image. These file types do not use pixels; therefore resolution does not apply to vector images.

Figures prepared as .doc/.docx or .jpeg/.jpg files will not be accepted.

Figure accessibility and alt text

Incorporating alt text (alternative text) when submitting your paper helps to foster inclusivity and accessibility. Good alt text ensures that individuals with visual impairments or those using screen readers can comprehend the content and context of your figures. The aim of alt text is to provide concise and informative descriptions of your figure so that all readers have access to the same level of information and understanding, and that all can engage with and benefit from the visual elements integral to scholarly content. Including alt text demonstrates a commitment to accessibility and enhances the overall impact and reach of your work.  

Alt text is applicable to all images, figures, illustrations, and photographs. 

Alt text is only accessible via e-reader and so it won’t appear as part of the typeset article. 

Detailed guidance on how to draft and submit alt text. 

Videos

• This journal accepts videos to be published as part of the article or supplementary material
• Videos should be submitted in MP4 format in possible
• All videos should have an accompanying legend

Graphical Abstract

Authors are encouraged to submit a graphical abstract or video abstract as part of the article, in addition to the text abstract. The graphical/video abstract should clearly summarize the focus and findings of the article. It will be published as part of the article online and in PDF, and used to promote your publication on our social media platforms. The graphical/video abstract should be submitted for peer review as a separate file, selecting the appropriate file-type designation in the journal’s online submission system. The file should be clearly named, e.g. graphical_abstract.tiff, video_abstract.mp4. Figures should be submitted as 300 dpi minimum resolution and 600 dpi maximum resolution, and have a maximum size of 8 cm wide x 6 cm high. See OUP’s 'Preparing your manuscript' page for guidance on appropriate file format and resolution for graphics and videos.

Supplementary Material

You must submit supplementary data or supplementary material at the same time as the main manuscript. Please ensure all supplementary material is submitted as a single PDF file, and adheres to the following guidelines:

• Supplementary material must be cited in the text of the main manuscript and labeled appropriately. For example, “Supplementary Table 1” or “Supplementary Figure 2”.
• Supplementary material will not be copyedited.
• Style and formatting of supplementary material should be consistent with that of the manuscript.
• Supplementary material should be formatted to function on any internet browser.
• Supplementary material files should be no larger than 2MB each.
• Additional computer scripts, data sets, video, structural models, etc. can be included as part of Supplementary Material.

Production

Licence to Publish and Open Access Options

PEDS offers the option of publishing under either a standard licence or an open access licence. Please note that some funders require open access publication as a condition of funding. If you are unsure whether you are required to publish open access, please do clarify any such requirements with your funder or institution.

Should you wish to publish your article open access, you should select your choice of open access licence in our online system after your article has been accepted for publication. You will need to pay an open access charge to publish under an open access licence.

Details of the open access licences and open access charges.

OUP has a growing number of Read and Publish agreements with institutions and consortia which provide funding for open access publishing. This means authors from participating institutions can publish open access, and the institution may pay the charge. Find out if your institution is participating.

Additional Author Resources

For additional information regarding submitting a manuscript, what to expect through the publication process, and guidance on how to promote your published article, please see our Author Resources.