Detailed Instructions for Authors of Protein Science

Table of Contents

Overview
Articles Published
Originality, Copyright, and Conflict of Interest
Manuscript Submission and Review
Submission of Revised and/or Accepted Manuscripts
Manuscript Elements and Order
1.Title page
2.Abstract and keywords
3.Abbreviations and symbols
4.Introduction
5.Results
6.Discussion
7.Materials and Methods (Note: This section follows Discussion section!)
8.Electronic Supplementary Material
9.Acknowledgments
10.References
11.Tables
12.Figure legends
13.Figures (artwork)
14.Cover Art
15.Electronic art submission
16.Supplementary material to appear in the Electronic Edition
17.Data Deposition Requirements: Protein and Nucleic Acid Sequences and Coordinates
Copyediting and Page Proofs
Page Charges and Color Art Charges
Funded Access Option
Offprints
Checklist for Manuscript Submission and Electronic Supplementary Material

 

Overview

Protein Science serves as an international forum for publishing original reports on proteins in the broadest sense. The journal aims to unify this field by cutting across established disciplinary lines and focusing on “protein-centered” science.
Protein Science encompasses the structure, function, and biochemical significance of proteins; their role in molecular and cell biology, genetics, and evolution; and their regulation and mechanisms of action. Representative topics include, but are not limited to, the structure of proteins and strategies of determining protein structure by chemical, biophysical, and recombinant methods; peptides; protein domains; protein folding and molecular dynamics; novel isolation procedures; enzyme action and regulation; interactions of proteins with nucleic acids, lipids, ligands, and other proteins; receptor-mediated signal transduction and other trans-membrane phenomena; the functions of proteins in replication, supramolecular assembly, immune reactions, development, and other biological processes; protein trafficking, synthesis, and sorting; and the recognition, localization, and signaling of proteins. In addition to the investigative techniques already mentioned, the journal will publish results of protein-centered work involving sequencing, modification, and mass spectrometry; cDNA, mutagenesis, and cloning; computational analysis; isolation and characterization; thermodynamics and hydrodynamics; kinetics; and equilibrium phenomena. Reports on the crystallization of proteins must provide novel information of general interest. Examples of novel information may include new approaches to expression or isolation of proteins in a form amenable to crystallization, novel conditions for crystallization that may be employed for other proteins, or new information related to the function of the protein. Research articles on computational or theoretical investigations on protein structure or function are encouraged. The article should be of general interest to the Protein Science community, and report results with a clear connection to a significant biological problem. The conclusions or predictions must be testable by a feasible experiment. Articles reporting new approaches to predict biologically relevant properties are encouraged; modifications of current algorithms without indication of significant improvements are not acceptable. Applications of molecular dynamics, homology modeling and other generally available program packages will not receive editorial support unless they provide biological insights which are clearly novel, and lead to experimentally testable hypotheses. Authors proposing predictive methods based e.g. on amino acid composition, or sequence, or 3D structure, are generally expected to make such methods available via a publicly accessible web server.
A primary consideration in judging the suitability of a manuscript is its originality and timeliness, the lack of which will be grounds for rejection, even if the work is well done from a technical perspective. Because judgments of originality and interest are inherently subjective, this policy implies that the editors and reviewers reserve the prerogative to decline publication on these grounds.

 

Articles Published

Protein Science publishes full-length original research papers as well as several other types of articles.
Full-Length Papers must report new findings that lead to significant advances in our understanding of the proteins of interest. The investigation should be at a point at which the major objectives have been accomplished and the findings can be convincingly presented in a concise article. Only the definitive evidence required to support the authors’ points should be presented; ancillary supporting data, if needed, should be deposited in the electronic supplement. Since Protein Science has contractual limitations on the number of pages it prints each year, it is very important that the articles be as concise as possible. Published full-length articles should not exceed about 5000 words of text plus a total of 10 figures, tables, or combination thereof. This corresponds to about 11 pages in the journal. It also corresponds to a submitted double-spaced manuscript with references, tables and figures not exceeding 30 pages.
Accelerated Communications are intended to provide an outlet for brief papers of exceptional importance and timeliness. The criteria for acceptance will be considerably more stringent than for full papers, and there will be a limit of 2,500 words in the body of the manuscript plus a maximum of four figures, tables, or combination thereof. The work must be complete and stand on its own merits. Accelerated Communications will be reviewed by one of the Editors and a member of the Editorial Advisory Board; every effort will be made to reach a decision within three weeks. The decision will be Accept or Reject (except for minor corrections), and accepted articles will be published in the next available issue of the journal. Manuscripts that exceed the size limits will be returned without review. The format may be continuous prose or divided into the traditional sections. All other procedures will be according to the Instructions for Authors.
Protein Structure Reports will be brief descriptions of new protein structures determined under Structural Genomics or other initiatives, typically not exceeding three to four printed pages in the journal (i.e. the complete submitted manuscript should not exceed about 10 pages including double-spaced text plus figures). As is the case for all articles published in Protein Science, Protein Structure Reports will be expected to include either novel biological or structural insights, or information that will be of interest to the readership of the journal. Because these articles will be very concise, the criteria may be relaxed somewhat relative to those that apply to full-length articles. In this context, authors may choose to describe several structures in a single report, in which case the relevance of the groups as a whole can be taken into consideration. In submitting multi-structure reports authors will be given discretion in including additional figures and text. Reports should contain a short abstract and keywords. Introductory and background material should be kept as brief as possible. Results and Discussion sections can be separate or combined. The Reports will typically include two figures and one table. One of the figures will be a stereo diagram showing the overall fold of the protein. Residue numbering will be included so that the path of the chain can be readily followed. For structures determined by NMR, this figure should show an ensemble of approximately 20 independently-derived backbone structures. The second, optional, figure may highlight a biologically-relevant or other interesting aspect of the structure. For structures determined by X-ray crystallography, the table will present data collection and refinement statistics, including the resolution and completeness of the data with agreement between equivalent intensity measurements. Statistics for the outer shell of data will also be given. The number of residues included in the refinement will be stated together with the number of solvent molecules, bound ions, and the like. Average B-factors for protein, solvent, and other atoms should be quoted. Values of the crystallographic R-factor and Rfree will be stated together with the discrepancy of the model from expected stereochemistry. The distribution of the Ramachandran angles among the categories defined by Laskowski et al. [Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993) J. Appl. Cryst. 26: 283-291] should be stated. For structures determined by NMR the number of distance or other restraints should be given together with the average departure from the value of the restraint. The discrepancies of the average structure from idealized geometry should also be summarized together with the distribution of the Ramachandran angles.
For the Record articles are intended to enable the publication of an interesting and important observation that should be in the literature. Articles reporting “one experiment” that are clearly part of a larger investigation are not appropriate. Similarly, success with a procedure that is not guaranteed to produce results (e.g., crystallization of a protein) is not appropriate unless the authors have employed novel approaches that will be applicable to other systems and thus of interest to a broader audience. The information must stand on its own merits. Manuscripts submitted to “For the Record” should contain a short abstract and keywords, and introduction and discussion sections (separate or combined) for a maximum of three journal pages (2500 words) in length. A single illustration conveying essential information, such as a protein sequence, is encouraged.
Reviews are intended to familiarize the general reader with the current status and future trends of rapidly evolving topics of current interest. Authors interested in submitting a Review should first send a letter of inquiry stating the title, scope, and tentative outline of the proposed article. We aim for an average length for Review articles of about eight printed pages and more concise manuscripts are encouraged (i.e. the complete submitted manuscript including figures and double-space text not to exceed about 30 pages). Reviews may also be solicited by the editorial staff. Reviews should include an Abstract of no more than 250 words and four to six keywords or short phrases for indexing. Reviews will be subject to evaluation similar to that for other contributions. Page charges are waived for invited reviews.
Recollections (usually by invitation) are historical reviews that are intended to give an overview of how the understanding of an interesting topic in Protein Science developed, including protein structure, protein properties, and general or specific biological roles of proteins. A contribution may be based largely on personal participation in research or may give a perspective of how knowledge in an area developed. The anecdotal accounts are intended to give insight and background usually lacking in conventional scientific papers. They may have an autobiographical flavor. Recollections can vary in length, with no specified format other than that a title, author’s name and affiliation, and a brief biographical sketch should be included. Usually figures and tables are not necessary but if included should have titles and legends. Inclusion of a few selected references is optional. One or more photographs may add interest. If a photograph has been previously published, written permission for its use must be included.

 

Originality, Copyright, and Conflict of Interest

One condition of publication is that all manuscripts submitted to Protein Science have not been published previously nor are they under consideration for publication elsewhere. Electronic publication open to viewers by subscription or by unrestricted access to a World Wide Web site is considered prior publication with the exception of dissertations mounted in electronic format by the library system of the degree-granting institution. Papers involving multiple authorship are reviewed with the understanding that all authors have approved the final submitted manuscript and concur in its submission to Protein Science. Copyrights to all papers must be assigned to The Protein Society by a signed Copyright Status Form before the Editor will transmit the paper for publication.
In the interests of candor and to help readers to detect potential bias, we now require authors of original research papers to declare any competing interests in relation to papers accepted for publication. Please submit one statement on behalf of all authors. Competing interests are defined as those that, through their potential influences on behavior or content or from perception of such potential influences, could undermine the objectivity, integrity or perceived value of a publication, or could embarrass the authors or the journal. They include, but are not limited to, any of the following:
Funding: Support for a research program (including salaries, equipment, supplies, reimbursement for attending symposia, and other expenses) by organizations that may gain or lose financially through publication of this paper.
Employment: Recent (i.e., while engaged in this research project), present, or anticipated employment by any organization that may gain or lose financially through publication of this paper.
Personal financial interests: Stocks or shares in companies that may gain or lose financially through publication; consultation fees or other forms of remuneration from organizations that may gain or lose financially; patents or patent applications whose value may be affected by publication.
It is difficult to specify a threshold at which a financial interest becomes significant, although we note that many US universities require faculty members to disclose interests exceeding 5% equity in a company.
We do not consider diversified mutual funds or investment trusts to constitute a competing financial interest.
We do not require authors to state the monetary value of their financial interests.

 

Manuscript Submission and Review

Manuscript submission. All Protein Science manuscripts must be submitted online via Manuscript Central at http://mc.manuscriptcentral.com/proteinscience. Please do not submit hard copies.

To find out if you have already created an account in Manuscript Central, enter your e-mail address in the "Password Help" field.

If you are submitting an article for the first time and/or do not have an existing account, carefully review the instructions posted under the heading "Resources" on the upper right hand side of log-in page; then click "Create Account" in the top right corner of the screen.

At the end of a successful submission, a confirmation screen with a manuscript number will appear and you will receive an e-mail confirming the manuscript has been received by the journal.

If you receive no confirmation, or if you experience technical difficulties during the submission process, click the "Get Help Now" link at the top-right corner of the log-in.
Each manuscript must be accompanied by a submission letter, copies of any related papers by the authors that are either submitted or in press, and the full names, E-mail addresses, telephone and FAX numbers, of at least six qualified reviewers. Authors may disqualify up to two potential reviewers. Authors are not required to be members of The Protein Society.
At the time of submission you will be asked to provide a 50-75 word statement outlining the importance and/or impact of the work presented in your manuscript to a broader audience. If your manuscript is accepted for publication in Protein Science, this brief summary may be used to prepare a highlight of your article to appear at the front of the issue of publication describing noteworthy papers ‘In This Issue.’

Please submit your manuscript as a Word or RTF file (for text and tables) and TIFF or EPS (for figures). Other file types are not suitable for production. Please note that Manuscript Central does not accept a single file upload from the author. Text, tables, and figures will need to be uploaded individually. Do not embed figures or tables in the document. Please note: This journal does not accept Microsoft WORD 2007 documents at this time. Please use WORD’s “Save As” option to save your document as an older (.doc) file type.
Manuscripts must be written in clear and concise English with double line spacing throughout (including title page, references, tables, and figure captions) and at least 1" (25 mm) margins on all sides. All pages must be numbered. A standard 12-point font should be used throughout. Please do not use any foreign language fonts (i.e., Chinese, Japanese) in the manuscript as they will not display properly. Do not use word hyphenation or text justification options.
LATeX Users: All files must be formatted in LaTeX version 2.02 or earlier. Figures must be formatted as either .TIFF or .EPS files and saved separately. Directory structures should not be used when referencing external files. This will cause a corrupted upload into Manuscript Central and will result in the cancellation of manuscript submission. Class and style files may be either internal or external. Manuscript Central provides all standard LaTeX class files for author use; however, you may create your own. Please be sure to check the log file provided at submission to see if you are missing the class file from your document.
LaTeX File Submission Guidelines: Upload a PDF version of your manuscript for review. Once a manuscript has been accepted for publication, zip-up the directory containing all your LaTeX files. This includes the TeX document, all graphics as separate files, any class files, any bibliography files, and the PDF of the final version. This zip file can be uploaded as a single file into Manuscript Central.
For technical assistance, please contact support@scholarone.com.
Correspondence: For submitted manuscripts, communication with the Editor will normally be via the online manuscript system. Correspondence can also be sent to:

Brian Matthews, Editor
Protein Science
Institute of Molecular Biology
1229 University of Oregon
1370 Franklin Boulevard
Eugene, OR 97403-1229, USA
Telephone: (541) 346-2572
Facsimile: (541) 346-5870
E-mail: proteinscience@proteinsociety.org
Review: Every effort will be made to decide whether the paper is appropriate for review within two weeks. Papers considered confirmatory or lacking sufficient originality will be returned without review. Most papers considered appropriate will be reviewed by at least two independent reviewers, one of whom may be a member of the Editorial Advisory Board. The Editor and/or the Associate Editors will make final selection of reviewers. If the reviewers disagree, or if in the judgment of the Editors the manuscript has not received adequate consideration, the manuscript and the reviewers’ opinions may be submitted to a member of the Editorial Advisory Board for arbitration. Editorial decisions that result from this process are usually final. The inability to identify referees willing to review a manuscript may be considered grounds for rejection.

 

Submission of Revised and/or Accepted Manuscripts

To streamline the entire review and publication process, authors are urged to follow the same formatting instructions for initial submission as for revision. For math objects within final submissions, please note that before submitting your Word file, make sure to UPDATE any embedded MathType objects in the file; otherwise, italics and other font specs might be lost. Double-check your Word manuscript visually to ensure the accuracy of fonts within the Word file.
When a manuscript requires revision, the corresponding author should resubmit the revised manuscript to the Web site within 21 days. Revisions returned after the requested period may be considered as new submissions.


 

Manuscript Elements and Order

Manuscripts should be organized in the following way, although papers prepared otherwise will be considered if there are clear and compelling reasons for variation. If authors choose an alternate order, justification for doing so must be included in the cover letter. All manuscript pages must be consecutively numbered.
1. Title page. The title should be concise and informative, but should avoid the use of acronyms and abbreviations. Include (a) full article title; (b) names and affiliations of all authors (matched by superscript numbers); (c) name, mailing address, telephone number, fax number, and E-mail address of the corresponding author; (d) running title of 50 characters or less; (e) list of total number of manuscript pages, supplementary material pages, tables, and figures; and (f) a description of supplementary material intended for publication in the Electronic Edition, including filenames.
2. Abstract and keywords. Include (a) an abstract of no more than 250 words, followed by (b) four to ten keywords or short phrases for indexing that reflect the content and major thrust of the paper, and (c) a 50-75-word statement, written for a broader audience, outlining the importance and/or impact of the work presented in the manuscript. The abstract should succinctly describe the objectives of the research, the experimental approach, and the major results and their significance. It must be self-explanatory and suitable for abstracting services such as Chemical Abstracts, Biosis, etc. Reference citations in the abstract should be avoided whenever possible and, if necessary, given in full. Avoid the use of abbreviations and acronyms in the abstract unless they are defined therein.
3. Abbreviations and symbols. Use standard abbreviations and acronyms and clearly define uncommon ones parenthetically within the text upon first appearance. The journal will accept standard Journal of Biological Chemistry abbreviations. If abbreviations are particularly complex or numerous, they may be collected into an abbreviations footnote, which will appear on the first or second page of the printed article. Greek symbols should be inserted directly from Word's "symbol insert" pulldown menu; equations/schemes should be inserted using MathType or Word's Equation Editor. 
4. Introduction.  The text of the paper begins on a new page. The Introduction should state the purpose of the investigation, the hypotheses tested, and the relationship to other work in the field. Avoid lengthy reviews of the literature.
5. Results. The results should be presented in a clear and concise manner, mentioning figures and tables that summarize or illustrate important findings.
6. Discussion. Briefly interpret the results and relate them to existing knowledge in the field, but do not merely restate the results or present reviews of the literature.
7. Materials and methods. Describe materials and methods briefly but in sufficient detail to allow others to repeat the experiments. Novel procedures should be described in detail, but published procedures should be referenced by a literature citation. If hazardous materials or dangerous procedures are employed, necessary precautions must be stated.
8. Electronic supplementary material. Describe briefly the supplementary material that is intended to be available over the Internet as part of the Electronic Edition of Protein Science. The names of all files should be given so that World Wide Web hyperlinks to them can be established within the Electronic Edition.
9. Acknowledgments. Research grants or other funding (including grant or project numbers as appropriate) may be acknowledged, as may significant contributions of individuals providing scholarly, technical, or clerical assistance.
10. References. Authors are asked to avoid extensive references. Protein Science uses the CBE reference style, numbered consecutively in order of appearance, and should be as complete as possible. All references cited in the text must be included in the References section and vice versa. Titles of journal articles and book chapters must be included; journal titles are abbreviated according to Chemical Abstracts Service Source Index, 1985. Page numbers must be inclusive. If a pre-existing coordinate set is used either in the research or to produce a figure, its databank file code should be given either in the caption or the Materials and Methods section, in addition to whatever literature references may be appropriate.
Please prepare the References list according to the following examples.

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

Book:
2. Voet D, Voet JG (1990) Biochemistry,  John Wiley & Sons, New York.

Book Chapter:
3. Gilmor ML, Rouse ST, Heilman CJ, Nash NR, Levey AI, Receptor fusion proteins and analysis. In: Ariano MA, Ed. (1998) Receptor localization.  Wiley-Liss, New York, pp 75-90.

Electronic Media:
4. Bio-Xplor, Version 1.0. New York: Biostructure Inc.; 1991.
Unpublished data and personal communications must be cited as such parenthetically in the text and must not appear in the References section. All citations of personal communications must be certified by letter from the communicating author.
Linking publish-ahead-of-print references. Authors can now have Medline links in their HTML references for citations that have only been published in EarlyView. Since EarlyView articles have PubMed records and a PubMed ID (PMID) is listed at the bottom of every PubMed record as the citation identifier, an author can include the PMID within their manuscript references as follows:
5. Wood CE, Appt SE, Clarkson TB, Franke AA, Lees CJ, Doerge DR, Cline JM. Effects of high-dose soy isoflavones and equol on reproductive tissues in female cynomolgus monkeys. PMID: 16723506 [Medline]
11. Tables. All tables must be cited in the text in numerical order and the approximate position of each indicated in the margin. Each table should be typed double-spaced on a separate page. Tables should be numbered consecutively with Roman numerals and grouped together after the References section. A short explanatory title, column headings, and (if necessary) footnotes should make the table intelligible without reference to the text. Vertical and diagonal rules should not be used in tables; instead, indentation and vertical or horizontal space should be used to group data. Large tables of an appendix nature may be considered for electronic publication in the Electronic Edition. If tables are reprinted from another source or if data included are from another source, permission to reprint is required. We cannot use tables produced in Excel at this time. Please produce all tables in your word processing program and save your manuscript whenever possible.
12. Figure legends. Type all figure legends double-spaced. Figure legends should be brief and should not contain methods. Each figure legend must begin with a short statement of the general content of the figure. Symbols indicated in the figure must be identified in the legend text. If figures are reprinted from another source, permission to reprint is required. Explain all symbols and abbreviations.
13. Figures (artwork). Please also read the Electronic Art Submission section. For digital artwork to be used for print publication, only .TIFF and .EPS files can be used. For the best reproduction, halftones should be high contrast. Line drawings, graphs, charts, and chemical formulae should be professionally prepared and labeled. Indicate magnification with a bar scale. Multipart figures should be submitted as one composite.
Figures should be kept to the minimum necessary to document results or methods that cannot be described in the text. Linear plots, particularly reciprocal velocity plots, should be avoided and replaced in the text in terms of slopes, intercepts, and standard deviations. All figures must be cited in the text in numerical order and the approximate position of each indicated in the margin. Most figures will be published in a single column of the Journal; use lettering of sufficient size to be legible after reduction (i.e., labels should be no smaller than 1.5–2 mm high in the reduced figure). Lettering of all figures within the article should be of uniform style (preferably a sans serif typeface). Use uppercase letters A, B, C, etc. to identify individual parts of multipart figures. Poor-quality figures or illegible labeling may result in delayed acceptance and publication. NOTE: Make sure the weight of all rules used in artwork is 1/2 point or heavier. Lighter-weight lines will not be picked up.
Stereo pairs must be mounted side by side. Corresponding points of the two images should be 6.3 cm apart.
The use of color is encouraged and justified when it significantly enhances communication and the understanding of the scientific data reported in the original manuscript. Note: Authors can save considerable costs to themselves and the journal by composing Figure 1A, B and C on a single page (or plate) rather than providing these on three separate pages (or plates). For instance, if one figure has three panels and each panel is on a separate page (or plate), then this figure will be counted as three color pages ($350 x 3). To avoid this, provide all three panels on one page (or plate). For best reproduction, bright, clear colors should be used; muted, "muddy" colors produce less satisfactory results. Dark colors against a dark background do not reproduce well. Lemon yellow (especially against a white background) tends to disappear; use slightly greenish or golden yellows instead.
14. Cover artwork. Authors are encouraged to submit a figure, related to their manuscript, which can be considered for use on the cover of the journal. This figure can be included as part of the initial submission, or included when the revised manuscript is being sent back to the Editor following receipt of comments from the referees.
15. Electronic Art Submission: Detailed Instructions
1. For final publication purposes, we can only accept your electronic art as an EPS or TIFF file. The following figure formats are unacceptable: JPG, GIF, PSD CRD, PCT, PPT, PDF, XLS, DOC, BMP, 123 (or other Lotus formats).
2. DO NOT EMBED FIGURES WITHIN THE MANUSCRIPT TEXT FILES or embed legends with the figures. If there are color keys to the figures, these should be included in the body of the figure rather than in the legend, as it can be difficult to match legend and figure colors.
3. Use Helvetica (or similar) typeface in point sizes no smaller than 8 pt and no larger than 10 pt, except for the main callouts (e.g. A, B, C), which should be 12 pt. It is best to avoid heavy letters, which often close up when reduced.
4. We cannot make any art corrections to TIFF or EPS files. All figures should be proof-read carefully before they are sent to us.
5. Line Art: Line art (without halftone dots) should be scanned or produced at a minimum of 1200 DPI in bitmap mode and saved as EPS files.
6. Halftone or Grayscale Art: Art to be reproduced as halftones should be scanned or produced at 300 DPI in grayscale mode and saved as TIFF files. This is for halftone/grayscale art only (art that doesn't also have line art within it). If within the halftone artwork there also exists line art, please follow the dpi specifications for Combo Art instead. When in doubt with halftone art, always default to the Combo Art specifications to ensure that halftone digital art will be used.
7. Combo Art: Combo art, which means both halftone art and line art within the same piece of art, must be 600 DPI in grayscale mode and saved as TIFF files.
8. Color Art: Note that color artwork is processed in CMYK format for print and processed in RGB format for online. To avoid delays at the page proof stage, authors are expected to have reviewed their artwork in both color formats prior to final submission. Final submission of electronic color artwork must be in CMYK (for print purposes), although online views of color artwork will be in RGB. Be aware that some color shifts between the two color modes are unavoidable. The resolution of your file must be a minimum of 300 DPI. Digital artwork must be created either in Photoshop or Illustrator and saved as either .EPS or .TIFF format (see more detailed guidelines below for digital artwork submissions). Color art to be reproduced as halftones should be scanned or produced at 300 DPI in CMYK mode and saved as TIFF files. Always save your color scans into the CMYK color space. Colors of similar shades should be avoided because, depending on final art sizing to conform to journal style, similar shades may be difficult to differentiate. Also, avoid using very light colors, since these typically don't reproduce well. Never submit color electronic files in the RGB mode. When color files are converted from RGB into CMYK the color can change significantly and type can be lost. Please convert any RBG files to CMYK files prior to submitting such artwork to make sure the file is correct.
For further guidance on preparing digital figure files, authors are encouraged to visit http://cjs.cadmus.com/da/applications.asp.
16. Supplementary material to appear in the Electronic Edition.
Authors are encouraged to request that lengthy tables and other data appear on the Protein Science Electronic Edition; such material will not be printed in the journal. In such cases, authors should include a short paragraph after the Materials and Methods section entitled “Electronic Supplementary Material” with a brief description of the content. Supply supplementary material in electronic form with the manuscript and describe it briefly (including filenames) at the bottom of the article title page. Electronic publication of supplementary material is strictly at the Editor’s discretion.
Supplementary tables for the Electronic Edition should be constructed, if possible, in a manner that will permit them to be read by common computer programs. They should be in plain ASCII without word processor formatting information. The tables should be constructed using a nonproportional spacing font such as Courier with close attention to spacing.
If it is not practical to construct supplementary tables in the ASCII format because special characters or elaborate layouts are essential for the presentation of the data, then formatted tables must be provided that can be read by standard word processor or spreadsheet software using IBM or Macintosh compatible computers.
Data that are best viewed in a graphical form should be submitted suitable for viewing by means of standard spreadsheet software. The files should be in plain ASCII text arranged as columns separated by tabs or commas. Each column should be identified by a short name or letter set off by double quotation marks, e.g. "X", "Y1", "Y2", etc. There should be a header paragraph with each line (80 characters maximum) enclosed in quotation marks that gives the titles of the X and Y axes and any other information that may be useful to the reader. Any other means of electronic publication of graphical material should be cleared in advance by the Editor and the Electronic Publishing Coordinator.
Graphical data that cannot be readily prepared as ASCII text may be provided as bitmap images, Microcal Origin data files, Jandel SigmaPlot data files, Lotus 123 or Excel spreadsheet files, or as standard word processing files containing embedded images. Any other means of electronic publication of graphical materials must be cleared in advance by the Editor and the Electronic Publishing Coordinator.
In the letter of submission, include a brief description of all Electronic Edition materials and indicate their desired treatment (provide this information as well at the bottom of the title page of the manuscript, including filenames). Electronic publication of such material is subject to availability of space and to the Editor’s discretion.
While abstract and reference files for the Electronic Edition will be prepared by the journal, preparation and submission of material for publication only in the Electronic Edition are the responsibility of the author.
17. Data Deposition Requirements.
Protein and Nucleic Acid Coordinates. Atomic coordinates and X-ray structure factors for three-dimensional protein structures must be deposited, before acceptance of the manuscript, with the Protein Data Bank (by FTP at ftp.rcsb.org or WWW at www.rcsb.org; fill out /pub/dep_form.txt) in order for a file identification code to be assigned and published in the article. Protein Science requires, as a condition for publication, that coordinates be publicly released no later than the publication date of the article. Coordinates may need to be made available for the reviewers. If so they will be treated confidentially, as any information in the papers under review.
Authors are strongly encouraged, but not required, to deposit in the Protein Data Bank NMR assignments and lists of NOE constraints and related data.
Data deposition requirements. Protein and Nucleic Acid Sequences. Protein sequence data must be deposited, prior to manuscript submission, with the Protein identification Resource (PIR) (National Biomedical Research Foundation, Georgetown University Medical Center, Washington, DC 20007, USA). Authors must certify in writing that this sequence has been scanned against this (or other comparable) database(s) and that all identities or significant similarities, including species variation, with other entries have been reported in the manuscript. Nucleotide sequence data must be included as part of manuscript submission and also, prior to manuscript acceptance, must be sent by the author to GenBank Submissions (M.S. K-710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA).

 

Copyediting and Page Proofs

The Publisher reserves the right to copyedit manuscripts to conform to Protein Science journal style. Wiley-Blackwell will send all page proofs electronically to corresponding authors. Digital page proofs (which include instructions and query sheet), together with an Author Packet of forms to be signed, will be distributed to corresponding authors online in PDF format. Each PDF proof will be accessible via a unique password that our compositor will send to the corresponding author in E-mail. Authors must review and return their PDF page proofs within 48 hours. Authors can opt to return these forms via e-mail, fax, or overnight mail. No rewriting of the final accepted manuscript is permitted at the proof stage. Excessive author alterations in proof may cause delays in publication and will be charged to the author.

 

Page Charges and Color Charges

Page Charges. Authors of accepted manuscripts will be assessed a page charge of US $40 per printed page for the first five pages and US $60 per page for each page over five. Authors will be billed at the time of proofing. Please note that all articles except for Invited Reviews are charged for page charges.
Color Charges. The reproduction of color artwork is partially subsidized by The Protein Society and in this connection the first page of color art will be provided free of charge to corresponding authors who are also Protein Society members, and all color in Invited Reviews is provided free of charge. With these exceptions, authors are expected to pay $350 per page of color to help defray this expense.

 

Funded Access Option

All papers are freely available online 12 months after publication. In addition, Protein Science is now offering an OnlineOpen option in which authors may pay a surcharge of $2500 (Protein Society Member Rate: $2000) to make their paper freely available online immediately upon publication. Authors may choose this option when page proofs are returned; choosing this option will have no effect on acceptance and publication of submitted papers. Click here for the OnlineOpen order form.

 

Offprints

With the page proofs, the corresponding author will receive a form to order offprints and copies of the complete issue at special contributor rates. Orders received after issue printing require special print runs and are subject to reprint charges (quotes will be provided on a case-by-case basis by the publisher).

 

Checklist for Manuscript Submission

___Full article title, authors, affiliations, and corresponding author’s mailing and e-mail addresses should be on a separate page.
___Eliminate nonstandard abbreviations in titles.
___Include with abstract brief statement outlining significance of the paper’s findings.
___Indicate institutional affiliation and complete mailing address for all authors.
___Identify corresponding author and supply telephone number, fax number, and e-mail address.
___Supply the names and contact information of at least six possible reviewers.
___Supply copies of any related articles submitted or in press.
___(Optional) Include a figure for consideration for use on the cover.
___Abstract and keywords should be on a separate page.
___Do not cite references, tables, or figures in the Abstract.
___Include written permission for any borrowed or modified figures or tables from the copyright holder.
___Supply full manufacturer names and addresses (city and state or country) for all brand name products cited in text.
___List figure legends as a group on a separate page.

___Make sure figures are of good quality.
___Do not cite materials submitted but not yet accepted for publication as References. Instead, cite in text as unpublished work
___Tables should not be saved in a graphic program; tables created using Word's table format are preferred.
___Supply tables on separate pages.
___Cite tables and figures in the text in numerical order.
___Check that references are in the style of the journal, accurate, and cited in the text.
___Ensure that Conflict of Interest Statement is included at the end of the manuscript file.
Electronic Supplementary Material (optional)
___Is the supplementary material indicated on the title page of the manuscript?.
___Is there a section after Materials and Methods entitled Electronic Supplementary Material?.
___Does the electronic supplementary material section briefly and adequately describe the supplementary material?
___Are the names of the supplementary material files in the DOS “8.3” format?