Proteins: Structure, Function, and Bioinformatics

 

Author Guidelines

  TABLE OF CONTENTS

1. Submission
2. Aims and Scope
3. Manuscript Categories and Requirements
4. Preparing the Submission
5. Editorial Policies and Ethical Considerations
6. Author Licensing
7. Publication Charges and Process After Acceptance
8. Post-Publication
9. Contact Details

  1. SUBMISSION

Authors should kindly note that submission of a paper will be held to imply that it is unpublished work which is not being considered for publication elsewhere. If accepted, it is expected that the paper will not be published in another journal or book in either the same or another format or language.

Once the submission has been prepared in accordance with the Author Guidelines, manuscripts should be submitted online. All new Proteins: Structure, Function, and Bioinformatics manuscripts are submitted through the Research Exchange submission portal. Should your manuscript proceed to the revision stage, you will be directed to make your revisions via the same submission portal. You may check the status of your submission at any time by logging on to submission.wiley.com and clicking the “My Submissions” button. For technical help with the submission system, please review our FAQs or contact [email protected].

The submission system will prompt the author to use an ORCID iD (a unique author identifier) to help distinguish their work from that of other researchers. Click here to find out more.

By submitting a manuscript to or reviewing for this publication, your name, email address, and affiliation, and other contact details the publication might require, will be used for the regular operations of the publication, including, when necessary, sharing with the publisher (Wiley) and partners for production and publication. The publication and the publisher recognize the importance of protecting the personal information collected from users in the operation of these services, and have practices in place to ensure that steps are taken to maintain the security, integrity, and privacy of the personal data collected and processed. You can learn more at https://authorservices.wiley.com/statements/data-protection-policy.html.

For help with submissions, please contact us at [email protected].

Preprints

PROTEINS: Structure, Function, and Bioinformatics will consider submissions that have previously been made available online, either on a preprint server like arXiv, bioRxiv, or PeerJ PrePrints, or on the authors’ own website. However, any such submissions must not have been published in a scientific journal, book or other venue that could be considered formal publication. Authors must inform the editorial office at submission if their paper has been made available as a preprint.

• Authors of accepted papers that were made available as preprints must be able to assign copyright to PROTEINS, or agree to the terms of the Wiley Open Access agreement and pay the associated fee.
• Given that the measurable impact of the article is diminished when citations are split between the preprint and the published article, authors are required to:
• Update the entry on the preprint server so that it links to and cites the DOI for the published version
• Cite only the published article themselves

Preprint your manuscript while it’s under review

You can now opt to seamlessly preprint your manuscript at submission, through Wiley’s Under Review service, powered by Authorea. Make your work citable and discoverable, before it is accepted or published. The Preprint portal for PROTEINS is available here: https://www.authorea.com/inst/20386. Learn more at Authorea's Under Review FAQ.

The under review service is powered by Authorea, an open research platform for all your research outputs, including data, figures, and preprints. By opting-in authors can:

• Seamlessly preprint at the same time you submit your research for publication
•  Share your work early, while indicating it is being considered at a specific journal 
• Track the peer review process openly in real time
• Immediately make their work citable, discoverable, and easily shareable 
• Get additional community feedback that can be used to improve your manuscript

Submitting your manuscript

Manuscripts can be uploaded either as a single document (containing the main text, tables and figures), or with figures and tables provided as separate files. Should your manuscript reach revision stage, figures and tables must be provided as separate files. The main manuscript file can be submitted in Microsoft Word (.doc or .docx) or LaTex (.tex) format.

If submitting your manuscript file in LaTex format via Research Exchange, select the file designation “Main Document – LaTeX .tex File” on upload. When submitting a Latex Main Document, you must also provide a PDF version of the manuscript for Peer Review. Please upload this file as “Main Document - LaTeX PDF.” All supporting files that are referred to in the Latex Main Document should be uploaded as a “LaTeX Supplementary File.”

• Be sure to upload all style sheets that are a part of the document.
• All images must be EPS files in order for the file to properly format.

Return to the Table of Contents

  2. AIMS AND SCOPE

PROTEINS: Structure, Function, and Bioinformatics publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS. In addition to full-length reports, short communications (usually not more than 4 printed pages) and prediction reports are welcome. Reviews are typically by invitation; authors are encouraged to submit proposed topics for consideration.

PROTEINS is bringing web-based technology to bear to speed and simplify the entire publication process. Proteins now offers online submission and peer review and encourages electronic submission of manuscripts, which expedites the review process. In addition, individual articles are published online as rapidly as possible after acceptance.

Return to the Table of Contents

  3. MANUSCRIPT CATEGORIES AND REQUIREMENTS

PROTEINS: Structure, Function, and Bioinformatics publishes the following contribution types:

• Research Articles
• Reviews
• Perspectives

Research Articles

This is the main avenue for publication of original research. Most of the articles published in any volume of PROTEINS are in the form of Research Articles. This form of publication is intended for reports of substantial research that make clear contributions that advance a field or a problem. We discourage submission of Research Articles based on material that is more appropriate for an archival journal.

Research Articles should be divided into the following sections: Introduction, Materials and Methods, Results, Discussion, and Conclusion (if applicable).

1. The Results and Discussion section can be combined into a single section when appropriate.

2. The manuscript should conform to standard scientific reporting style.

3. Sufficient data and information must be given so that the study can be replicated.

Reviews

Reviews contribute critical assessment of interesting and important problems or fields. Authors wishing to submit reviews are encouraged to contact the Editor-in-Chief for approval prior to submission. All Reviews in PROTEINS are peer-reviewed.

Perspectives

Previously known as Research Commentary, the Perspectives section is intended for opinion pieces in a range of styles. The goal of this section is to foment presentation of controversial ideas, critical evaluation of concepts, idiosyncratic viewpoints, and challenges to ideas. Didactic pieces and historical and biographical accounts will also be considered.

Return to the Table of Contents

  4. PREPARING THE SUBMISSION

Free Format submission

Proteins now offers Free Format submission for a simplified and streamlined submission process.

Before you submit, you will need:

• Your manuscript: this should be an editable file including text, figures, and tables, or separate files – whichever you prefer. All required sections should be contained in your manuscript, including abstract, introduction, methods, results, and conclusions. Figures and tables should have legends. Figures should be uploaded in the highest resolution possible. References may be submitted in any style or format, as long as it is consistent throughout the manuscript. Supporting information should be submitted in separate files. If the manuscript, figures or tables are difficult for you to read, they will also be difficult for the editors and reviewers, and the editorial office will send it back to you for revision. Your manuscript may also be sent back to you for revision if the quality of English language is poor.
• An ORCID ID, freely available at https://orcid.org. (Why is this important? Your article, if accepted and published, will be attached to your ORCID profile. Institutions and funders are increasingly requiring authors to have ORCID IDs.)
• The title page of the manuscript, including:
  • Your co-author details, including affiliation and email address. (Why is this important? We need to keep all co-authors informed of the outcome of the peer review process.)
  • Statements relating to our ethics and integrity policies, which may include any of the following (Why are these important? We need to uphold rigorous ethical standards for the research we consider for publication):
    • data availability statement
    • funding statement
    • conflict of interest disclosure
    • ethics approval statement
    • patient consent statement
    • permission to reproduce material from other sources
    • clinical trial registration

Cover Letters

Cover letters are not mandatory; however, they may be supplied at the author’s discretion.

Submission File(s)
Manuscripts can be uploaded either as a single document (containing the main text, tables and figures), or with figures and tables provided as separate files. Should your manuscript reach revision stage, figures and tables must be provided as separate files. The main manuscript file can be submitted in Microsoft Word (.doc or .docx) or LaTex (.tex) format.

Your main document file should include (please see below for details):

• A short informative title containing the major key words. The title should not contain abbreviations (see Wiley's best practice SEO tips). The tile should be 16 words or less;
• A short running title of less than 40 characters;
• The full names of the authors;
• The author's institutional affiliations where the work was conducted, with a footnote for the author’s present address if different from where the work was conducted;
• Corresponding author information;
• Acknowledgments;
• Abstract and keywords;
• Main text,  formatted as introduction, materials & methods, results, discussion, conclusion;
• References;
• Tables (each table complete with title and footnotes);
• Figure legends must be added beneath each individual image during upload AND as a complete list in the text;
• Figures;
• Appendices (if relevant);
• Supporting information (submit as separate file if it includes a large data set or movie files)
• Data Availability Statement
• Conflict of interest statement

 

Authorship

Please refer to PROTEINS’s Authorship policy in the Editorial Policies and Ethical Considerations section for details on author listing eligibility.

Acknowledgements

Contributions from anyone who does not meet the criteria for authorship should be listed, with permission from the contributor, in an Acknowledgments section. Financial and material support should also be mentioned. Thanks to anonymous reviewers are not appropriate.

Conflict of Interest Statement

Authors will be asked to provide a conflict of interest statement during the submission process. For details on what to include in this section, see the ‘Conflict of Interest’ section in the Editorial Policies and Ethical Considerations section below. Submitting authors should ensure they liaise with all co-authors to confirm agreement with the final statement.

Abstract

This should summarize the purpose, methods, results, and major conclusions of the work. A 250 word limit will be strictly enforced. Please provide main keywords.

Keywords

Please provide up to 5-7 keywords. Keywords should be taken from those recommended by the US National Library of Medicine's Medical Subject Headings (MeSH) browser list at www.nlm.nih.gov/mesh.

Main Text

• The PROTEINS uses British/US spelling; however, authors may submit using either option, as spelling of accepted papers is converted during the production process.
• Footnotes to the text are not allowed and any such material should be incorporated into the text as parenthetical matter.

References

All references should be numbered consecutively in order of appearance and should be as complete as possible. In text citations should cite references in consecutive order using Arabic superscript numerals. For more information about this reference style, please see the AMA Manual of Style.

Reference examples follow:

Journal article
1. King VM, Armstrong DM, Apps R, Trott JR. Numerical aspects of pontine, lateral reticular, and inferior olivary projections to two paravermal cortical zones of the cat cerebellum. J Comp Neurol 1998;390:537-551.

Book
2. Voet D, Voet JG. Biochemistry. New York: John Wiley & Sons; 1990. 1223 p. Please note that journal title abbreviations should conform to the practices of Chemical Abstracts.

Internet Document
9. American Cancer Society. Cancer Facts & Figures 2003. http://www.cancer.org/downloads/STT/CAFF2003PWSecured.pdf. Accessed March 3, 2003.

Endnotes

Endnotes should be placed as a list at the end of the paper only, not at the foot of each page. They should be numbered in the list and referred to in the text with consecutive, superscript Arabic numerals. Keep endnotes brief; they should contain only short comments tangential to the main argument of the paper.

Footnotes

Footnotes should be placed as a list at the end of the paper only, not at the foot of each page. They should be numbered in the list and referred to in the text with consecutive, superscript Arabic numerals. Keep footnotes brief; they should contain only short comments tangential to the main argument of the paper and should not include references.

Figure Legends

Legends should be concise but comprehensive—the figure and its legend must be understandable without reference to the text. Include definitions of any symbols used and define/explain all abbreviations and units of measurement.

Tables

Tables should be self-contained and complement, not duplicate, information contained in the text. They should be supplied as editable files, not pasted as images. Legends should be concise but comprehensive – the table, legend, and footnotes must be understandable without reference to the text. All abbreviations must be defined in footnotes. Footnote symbols: †, ‡, §, ¶, should be used (in that order) and *, **, *** should be reserved for P-values. Statistical measures such as SD or SEM should be identified in the headings.

Figures

Although authors are encouraged to send the highest-quality figures possible, figures can be submitted in any format provided they are legible, easy to read, and visible in the manuscript PDF at every stage of peer review. If a different format is required for publication, the Production Editor will request the figure(s) in a different file type after acceptance.

Color Figures

Figures submitted in color may be reproduced in color free of charge. Please note, however, that it is preferable that line figures (e.g. graphs and charts) are supplied in black and white so that they are legible if printed by a reader in black and white.

Supporting Information

Authors may submit Supporting Information for their articles to be posted in the electronic version of the journal. These materials must be submitted online using the File Designation “Supplementary Material for Review.” Supporting text, tables and figures must be in PDF format. The only exceptions are audio and moving image files, which should be submitted in .mov or .mp3 format.

Click here for Wiley’s FAQs on supporting information.

Note: if data, scripts, or other artefacts used to generate the analyses presented in the paper are available via a publicly available data repository, authors should include a reference to the location of the material within their paper.

General Style Points

The following points provide general advice on formatting and style.

• Abbreviations: In general, terms should not be abbreviated unless they are used repeatedly and the abbreviation is helpful to the reader. Initially, use the word in full, followed by the abbreviation in parentheses. Thereafter use the abbreviation only.
• Units of measurement: Measurements should be given in SI or SI-derived units. Visit the Bureau International des Poids et Mesures (BIPM) website for more information about SI units.
• Numbers: Numbers under 10 are spelt out, except for: measurements with a unit (8mmol/l); age (6 weeks old), or lists with other numbers (11 dogs, 9 cats, 4 gerbils).
• Trade Names: Chemical substances should be referred to by the generic name only. Trade names should not be used. Drugs should be referred to by their generic names. If proprietary drugs have been used in the study, refer to these by their generic name, mentioning the proprietary name and the name and location of the manufacturer in parentheses.

Resource Identification Initiative

PROTEINS  supports the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. This initiative, led by the Neuroscience Information Framework and the Oregon Health & Science University Library, provides unique identifiers for antibodies, model organisms, cell lines, and tools including software and databases. These IDs, called Research Resource Identifiers (RRIDs), are machine-readable and can be used to search for all papers where a particular resource was used and to increase access to critical data to help researchers identify suitable reagents and tools.

Authors are asked to use RRIDs to cite the resources used in their research where applicable in the text, similar to a regular citation or Genbank Accession number. For antibodies, authors should include in the citation the vendor, catalogue number, and RRID both in the text upon first mention in the Methods section. For software tools and databases, please provide the name of the resource followed by the resource website, if available, and the RRID. For model organisms, the RRID alone is sufficient.

Additionally, authors must include the RIIDs in the list of keywords associated with the manuscript.

To Obtain Research Resource Identifiers (RRIDs):

1. Use the Resource Identification Portal, created by the Resource Identification Initiative Working Group.
2. Search for the research resource (please see the section titled “Search Features and Tips” for more information).
3. Click on the “Cite This” button to obtain the citation and insert the citation into the manuscript text.

If there is a resource that is not found within the Portal, authors are asked to register the resource with the appropriate resource authority. Information on how to do this is provided in the “Resource Citation Guidelines” section of the Portal.

If any difficulties in obtaining identifiers arise, please contact [email protected] for assistance.

Example Citations:

Antibodies: "Wnt3 was localized using a rabbit polyclonal antibody C64F2 against Wnt3 (Cell Signaling Technology, Cat# 2721S, RRID: AB_2215411)"

Model Organisms: "Experiments were conducted in c. elegans strain SP304 (RRID:CGC_SP304)"

Cell lines: "Experiments were conducted in PC12 CLS cells (CLS Cat# 500311/p701_PC-12, RRID:CVCL_0481)"

Tools, Software, and Databases: "Image analysis was conducted with CellProfiler Image Analysis Software, V2.0 (http://www.cellprofiler.org, RRID:nif-0000-00280)"

Wiley Author Resources

Manuscript Preparation Tips: Wiley has a range of resources for authors preparing manuscripts for submission available here. In particular, we encourage authors to consult Wiley’s best practice tips on Writing for Search Engine Optimization.

Editing, Translation, and Formatting Support: Wiley Editing Services can greatly improve the chances of a manuscript being accepted. Offering expert help in English language editing, translation, manuscript formatting, and figure preparation, Wiley Editing Services ensures that the manuscript is ready for submission.

Refer and Transfer Program

This journal participates in Wiley’s Refer & Transfer program.

If your manuscript is not accepted at your first choice journal, you may receive a recommendation to transfer the manuscript to another suitable Wiley journal, either through a referral from the journal’s editor or through our Transfer Desk Assistant.

  5. EDITORIAL POLICIES AND ETHICAL CONSIDERATIONS

Peer Review and Acceptance

The acceptance criteria for all papers are the quality and originality of the research and its significance to journal readership. Except where otherwise stated, manuscripts are single-blind peer reviewed. Papers will only be sent to review if the Editor-in-Chief determines that the paper meets the appropriate quality and relevance requirements.

Wiley's policy on the confidentiality of the review process is available here.

Transparent Peer Review: This journal is participating in a pilot on Peer Review Transparency. By submitting to this journal, authors agree that the reviewer reports, their responses, and the editor’s decision letter will be linked from the published article to where they appear on Publons in the case that the article is accepted. Authors have the opportunity to opt out during submission, and reviewers may remain anonymous unless they would like to sign their report.

 

Human Studies and Subjects

For manuscripts reporting medical studies that involve human participants, a statement identifying the ethics committee that approved the study and confirmation that the study conforms to recognized standards is required, for example: Declaration of Helsinki; US Federal Policy for the Protection of Human Subjects; or European Medicines Agency Guidelines for Good Clinical Practice. It should also state clearly in the text that all persons gave their informed consent prior to their inclusion in the study.

Patient anonymity should be preserved. Photographs need to be cropped sufficiently to prevent human subjects being recognized (or an eye bar should be used). Images and information from individual participants will only be published where the authors have obtained the individual's free prior informed consent. Authors do not need to provide a copy of the consent form to the publisher; however, in signing the author license to publish, authors are required to confirm that consent has been obtained. Wiley has a standard patient consent form available for use.

Animal Studies

A statement indicating that the protocol and procedures employed were ethically reviewed and approved, as well as the name of the body giving approval, must be included in the Methods section of the manuscript. Authors are encouraged to adhere to animal research reporting standards, for example the ARRIVE guidelines for reporting study design and statistical analysis; experimental procedures; experimental animals and housing and husbandry. Authors should also state whether experiments were performed in accordance with relevant institutional and national guidelines for the care and use of laboratory animals:

• US authors should cite compliance with the US National Research Council's Guide for the Care and Use of Laboratory Animals, the US Public Health Service's Policy on Humane Care and Use of Laboratory Animals, and Guide for the Care and Use of Laboratory Animals.
• UK authors should conform to UK legislation under the Animals (Scientific Procedures) Act 1986 Amendment Regulations (SI 2012/3039).
• European authors outside the UK should conform to Directive 2010/63/EU.

Clinical Trial Registration

PROTEINS requires that clinical trials are prospectively registered in a publicly accessible database and clinical trial registration numbers should be included in all papers that report their results. Authors are asked to include the name of the trial register and the clinical trial registration number at the end of the abstract. If the trial is not registered, or was registered retrospectively, the reasons for this should be explained.

Research Reporting Guidelines

Accurate and complete reporting enables readers to fully appraise research, replicate it, and use it. Authors are encouraged to adhere to recognized research reporting standards. The EQUATOR Network collects more than 370 reporting guidelines for many study types, including for:

• Randomised trials: CONSORT
• Observational studies: STROBE
• Systematic reviews: PRISMA
• Case reports: CARE
• Qualitative research: SRQR
• Diagnostic / prognostic studies: STARD
• Quality improvement studies: SQUIRE
• Economic evaluations: CHEERS
• Animal pre-clinical studies: ARRIVE
• Study protocols: SPIRIT
• Clinical practice guidelines: AGREE

We also encourage authors to refer to and follow guidelines from:

• Future of Research Communications and e-Scholarship (FORCE11)
• National Research Council's Institute for Laboratory Animal Research guidelines
• The Gold Standard Publication Checklist from Hooijmans and colleagues
• Minimum Information Guidelines from Diverse Bioscience Communities (MIBBI) website
• FAIRsharing website

Species Names

Upon its first use in the title, abstract and text, the common name of a species should be followed by the scientific name (genus, species and authority) in parentheses. For well-known species, however, scientific names may be omitted from article titles. If no common name exists in English, the scientific name should be used only.

Genetic Nomenclature

Sequence variants should be described in the text and tables using both DNA and protein designations whenever appropriate. Sequence variant nomenclature must follow the current HGVS guidelines; examples of acceptable nomenclature are provided here: varnomen.hgvs.org.

Sequence Data

Nucleotide sequence data can be submitted in electronic form to any of the three major collaborative databases: DDBJ, EMBL or GenBank. It is only necessary to submit to one database as data are exchanged between DDBJ, EMBL and GenBank on a daily basis. The suggested wording for referring to accession-number information is: ‘These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession number #####’. Addresses are as follows:

• DNA Data Bank of Japan (DDBJ): www.ddbj.nig.ac.jp
• EMBL Nucleotide Archive: www.ebi.ac.uk/ena
• GenBank: www.ncbi.nlm.nih.gov/genbank

Proteins sequence data should be submitted to either of the following repositories:

• Protein Information Resource (PIR): pir.georgetown.edu
• SWISS-PROT: www.expasy.ch/sprot/sprot-top

Crystallographic Structures

A good summary of structure validation can be found in the article by Gerard Kleywegt, Acta Cryst. (2000) D 56, 249-265.

For all crystallographic studies, coordinates and structure factors should be deposited in the Protein Data Bank at the time of manuscript submission. The PDB id(s) should be included in the text.

For all crystal structures the following data must be summarized in one Table:

1. The space group, unit cell dimensions, the Wilson plot B value for the data and the effective resolution.
2. The effective resolution should be described clearly by quoting the following crystallographic indicators for the entire data set and for the highest resolution shell (shown in parentheses): (i) the completeness of the data set; (ii) the internal agreement of the data (Rmerge); (iii) the average I/σ (I)value; (iv) the redundancy of the collected data (reflections measured divided by the number of unique reflections).
3. The absolute number of unique reflections observed (after merging), number of measured reflections (before merging) and the number of unique reflections used in the Rfree set.
4. If crystallographic twining was detected, the twin law and the twin percentage should be clearly shown.
5. For the refinement statistics, the crystallographic R-factor and the corresponding Rfree should be quoted along with the number of molecules of each type that are present in the asymmetric unit.The total number of atoms in the biological molecules related by non-crystallographic symmetry must be given, as well as the number of ions, water molecules, and ligands.For each of these classes of molecules the average B factors should be given.The RMS deviations from ideal geometry (and ideally the RMSZ score reported by modern refinement software) should be given for bonds and angles).In the cases of TLS refinement the number of TLS bodies should also be included in the table.
6. For validation we strongly encourage all authors to use the free MolProbity software that is available on the web (http://molprobity.biochem.duke.edu), Davis et al (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35: W375-W383).The following indicators are required to be tabulated: (i) the percentage of residues that are outliers in the Ramachandran plot, (ii) the percentage of residues that are in favored regions of the Ramachandran plot, and (iii) the percentage of rotamer outliers.

The Methods section should provide adequate details regard the steps followed in constructing the model and refining the structure, with appropriate citations to all software used:

1. For molecular replacement solutions, the way that the search model was constructed should be explained, quoting the PDB IDs of the search model(s).
2. For heavy atom phasing, details on each dataset used should be provided as additional columns for all items in sections 1-4 of the main Table described above.However, the completeness (i) and the redundancy (iv) should be quoted also treating Friedel pairs as separate observations (as items v and vi).Indications about the initial map quality can be given in the text.
3. The history and salient details of the refinement methods employed: the type of restraints used, a description of how the thermal parameters were treated, and how solvent sites were selected and handled during refinement.

Any structural features that are considered somewhat unusual should be described.Examples include: cis-peptide bonds, unoccupied volume inside the protein, buried ionizable groups that are not involved in salt bridges or reasonable hydrogen-bonding environments, unusual locations of glycine and proline residues, and unusual distribution of polar and hydrophobic groups within the molecule.

Structures from NMR Spectroscopy

A composite Figure may include (i) multiple sequence alignment, and (ii) stereoview of a ribbon representation of the structure.All secondary structural elements and the N- and the C-termini of the protein should be clearly labeled on the structure.Other sub-figures or a second figure could include other structural information, such as a depiction of the structural ensemble, conserved surface and/or electrostatic surface images, or comparison with similar or homologous protein structures.A stereo image of a superimposed ensemble of 10-20 conformers must be included either as a subfigure or as a Supporting Figure. A Table of structural statistics describing the overall quality of the structure should be included, and it can be submitted as a Supporting Table.It should include summaries of NMR assignment completeness statistics, a summary of constraint types and their distributions, summaries of constraint violations, backbone and heavy atom RMSDs (with ordered-residue ranges defined), deviations from ideal geometry, and other structure quality statistics (e.g. Ramachandran, ProCheck-NMR, and/or MolProbity statistics).

Deposition of data: In addition to the atomic coordinates, the list of assigned chemical shift, the list of NOESY peaks (if appropriate), and the complete list of experimental constraints data used in the last round of refinement must be deposited with the PDB and BMRB.The PDB and BMRD identifier codes must be provided in the main text.Hydrogen bonding patterns within the protein should be described, with particular attention to unsatisfied buried main chain hydrogen bonds.A good summary of protein NMR structure validation can be found in the article by Bhattacharya et al. PROTEINS (2007) 66: 778-795.Any structural features that are considered somewhat unusual should be described.

In addition to the atomic coordinates, the following data should also be deposited with the PDB and BMRB:list of assigned chemical shifts, list of NOESY peaks (if appropriate), and complete list of experimental constraints used in the last round of refinement. The PDB and BioMagResDB identifier codes must be provided in the main text.

Database Linking

For papers describing structures of biological macromolecules, the atomic coordinates and the related experimental data (structure factor amplitudes/intensities and/or NMR restraints) must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/pdbe), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu). The PDB ID must be included in the manuscript and entered into the designated field in the submission system. Authors must agree to release the atomic coordinates and experimental data when the associated article is published.Questions relating to depositions should be sent to [email protected]. Authors are strongly encouraged to submit genetic and protein database information with their manuscript for the databases listed below and a hypertext link will appear in the online version of the article, via Wiley Online Library at /.

• The Genome Database (GDB)
• Protein Databank (PDB)
• Genbank
• Online Mendelian Inheritance in Man (OMIM)
• Molecular Modeling Database (MMDB)
• Entrez Genomes
• Entrez Proteins
• European Molecular Biology Laboratory (EMBL)
• SpecInfo
• ExPasy
• SWISS-PROT

1. To create hypertext links, authors must supply the gene name as it appears in the article, the database where the record appears, and the database specific identification number or name.

2. Please follow the instructions in the Database Linking Submittal Form, and submit a copy of that form with your manuscript.

3. It is the responsibility of the author(s) to ensure that the database information that is provided with the manuscript is correct and up to date.

4. The publisher will not submit new information to the databases. Incorrect information will result in the omission of hypertext links in the article.

5. For those articles containing gene and protein sequence information with a corresponding database record (see list of databases) hyperlinked database queries will be added to the online version for the full-text HTML version of the journal.

6. The hypertext links will appear in the Special Content Links section of the Abstract page, the text of the abstract and throughout the full text of the article.

Conflict of Interest

PROTEINS requires that all authors disclose any potential sources of conflict of interest. Any interest or relationship, financial or otherwise that might be perceived as influencing an author's objectivity is considered a potential source of conflict of interest. These must be disclosed when directly relevant or directly related to the work that the authors describe in their man uscript. Potential sources of conflict of interest include, but are not limited to: patent or stock ownership, membership of a company board of directors, membership of an advisory board or committee for a company, and consultancy for or receipt of speaker's fees from a company. The existence of a conflict of interest does not preclude publication. If the authors have no conflict of interest to declare, they must also state this at submission. It is the responsibility of the corresponding author to review this policy with all authors and collectively to disclose with the submission ALL pertinent commercial and other relationships.

Funding

Authors should list all funding sources in the Acknowledgments section. Authors are responsible for the accuracy of their funder designation. If in doubt, please check the Open Funder Registry for the correct nomenclature: https://www.crossref.org/services/funder-registry/

Authorship

The list of authors should accurately illustrate who contributed to the work and how. All those listed as authors should qualify for authorship according to the following criteria:

1. Have made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; and
2. Been involved in drafting the manuscript or revising it critically for important intellectual content; and
3. Given final approval of the version to be published. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content; and
4. Agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Contributions from anyone who does not meet the criteria for authorship should be listed, with permission from the contributor, in an Acknowledgments section (for example, to recognize contributions from people who provided technical help, collation of data, writing assistance, acquisition of funding, or a department chairperson who provided general support). Prior to submitting the article all authors should agree on the order in which their names will be listed in the manuscript.

Joint first or senior authorship: In the case of joint first authorship a footnote should be added to the author listing, e.g. ‘X and Y should be considered joint first author’ or ‘X and Y should be considered joint senior author.’

Data Sharing and Data Accessibility

PROTEINS expects data sharing. Review Wiley’s Data Sharing policy where you will be able to see and select the data availability statement that is right for your submission. 

Publication Ethics

PROTEINS is a member of the Committee on Publication Ethics (COPE). Note PROTEINS uses iThenticate’s CrossCheck software to detect instances of overlapping and similar text in submitted manuscripts. Read Wiley’s Top 10 Publishing Ethics Tips for Authors here. Wiley’s Publication Ethics Guidelines can be found here.

ORCID

As part of PROTEINS’s commitment to supporting authors at every step of the publishing process, the journal requires the submitting author (only) to provide an ORCID iD when submitting a manuscript. This takes around 2 minutes to complete. Find more information here.

  6. AUTHOR LICENSING

If a paper is accepted for publication, the author identified as the formal corresponding author will receive an email prompting them to log in to Author Services, where via the Wiley Author Licensing Service (WALS) they will be required to complete a copyright license agreement on behalf of all authors of the paper.

Authors may choose to publish under the terms of the journal’s standard copyright agreement, or Open Access under the terms of a Creative Commons License.

General information regarding licensing and copyright is available here. To review the Creative Commons License options offered under Open Access, please click here. (Note that certain funders mandate a particular type of CC license be used; to check this please click here.)

Self-Archiving Definitions and Policies: Note that the journal’s standard copyright agreement allows for self-archiving of different versions of the article under specific conditions. Please click here for more detailed information about self-archiving definitions and policies.

Open Access: PROTEINS offers authors the ability to publish their articles Open Access: immediately free to read, download, and share. Authors who choose to publish their article as Open Access will be charged an Article Publication Charge (APC). Authors whose institutions have paid the Wiley Open Access partner fee are eligible for a discount on the publication charge and on acceptance a discounted fee is payable by the author. Please see Wiley’s pages on agreements with Funders, Institutions and our Author Compliance Tool to find out more about what arrangements your funder may have made to pay for Open Access. For more information on this journal’s APCs, please see the Open Access page.

Funder Open Access: Please click here for more information on Wiley’s compliance with specific Funder Open Access Policies.

  7. PUBLICATION CHARGES AND PROCESS AFTER ACCEPTANCE

Accepted Article Received in Production

When an accepted article is received by Wiley’s production team, the corresponding author will receive an email asking them to login or register with Wiley Author Services. They will be asked to sign a publication license at this point.

Proofs

Once the paper has been typeset, the author will receive an email notification of the URL from where to download the typeset page proofs of the article in PDF format; associated forms and full instructions on how to correct and return the file are also provided.

Authors are responsible for all statements made in their work, including changes made during the editorial process and thus the proofs must be checked carefully. Note that proofs should be returned within 48 hours from receipt.

Publication Charges

There are no mandatory charges to authors publishing in PROTEINS.

Authors may choose to publish in an open access format which carries an Article Publication Charge (APC). For more information on this journal’s APCs, please see the Open Access page.

Early View

PROTEINS offers rapid publication via Wiley’s Early View service. Early View articles (first online Version of Record) are published on Wiley Online Library before inclusion in an issue of PROTEINS. Note there may be a delay after corrections are received before the article appears online, as the proofs are carefully reviewed. Once the article is published in Early View, no further changes to the article are possible. The Early View article is fully citable using the Digital Object Identifier (DOI) and carries an online publication date.

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  8. POST PUBLICATION

Access and Sharing

When an article is published online:

• The author will receive an email alert (if requested).
• Authors can share a link to their published article through social media.
• The author will have free access to the paper (after accepting the Terms & Conditions of use, they can view the article).
• For non-Open Access articles, a PDF File of the final article is available to corresponding authors and authors can share a link to access their paper with an unlimited number of colleagues. More information is available on Wiley Author Services.

Promoting an Article

A video abstract can be a quick way to make the message of your research accessible to a much larger audience. Wiley and its partner Research Square offer a service of professionally produced video abstracts, available to authors of articles accepted in PROTEINS. You can learn more about it here. If you have any questions, please direct them to [email protected].

For ideas and guidance on how to self-promote a research article, authors should visit Wiley Author Services.

Measuring the Impact of an Article

Wiley helps authors to measure the impact of their research. Learn more at https://authorservices.wiley.com/author-resources/Journal-Authors/Promotion/index.html.

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  9. CONTACT DETAILS

A complete list of contacts for PROTEINS is available on the journal’s Contacts page.

 

Author Guidelines updated July, 2025

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