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# JBC: Instructions for Authors

Table of Content

How to submit

Submission Fee
Initial Manuscript Submission
Revised Manuscript Submission
Accelerated Publication Submission
Final Submission of an Accepted Manuscript

Organization of the Manuscript

Text
References
Tables and Figures
RGB Workflow
Supplemental Data

Publication Charges

> Page Charges
> Color Figures
> Halftones
> Reprints

Chemical and Mathematical Usage
Protein and Nucleic Acid Sequences
Genomic and Proteomic Studies
Crystallographic Studies
Database Accession Hyperlinks For JBC On-line

## General Requirements

All submitted manuscripts should contain original research not previously published and not under consideration for publication elsewhere. Papers may come from any country but must be written in English. All submissions must be accompanied by abstracts of the authors' manuscripts on related subjects that are in press or currently under editorial review. Electronic reprints of related published papers by the authors or manuscripts in press may also be helpful to the reviewers.

Manuscripts may be submitted for consideration as Regular Papers or Accelerated Publications. The JOURNAL also publishes Minireviews, all of which are by invitation only. Authors are urged to keep the length of Regular Papers to six printed pages or less. Accelerated Publications can be no longer than five printed pages, including all spaces, references, figures and tables. A five page paper is usually less than 30,000 characters plus two figures or tables (if each figure or table is less than 1/4 page).

# How to Submit

##### Submission Fee: Beginning September 12, 2006 there will be a one-time mandatory submission fee of $60 for each article submitted.

#### Authors are required to submit manuscripts electronically using the Online Submission and Review System (OSRS) available at http://www.jbc.org/submit. All manuscript must be submitted in PDF format.

## Submission Fee

There will be a one-time mandatory submission fee of $60 for each article submitted. Manuscripts will not be processed until the fee is received.

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## Initial Manuscript Submission

1. Prepare the text in Microsoft Word 6.0 (Word 2001 for Mac) or a later version.

In preparing the Word text document create a format that produces a manuscript that has an appearance similar to that of a published paper. If your paper is accepted, a PDF version of the manuscript is published as JBC Papers in Press and the effort of formatting will yield a more attractive, readable publication. The document should have the approximate appearance and layout shown (details below):

See a complete example of the manuscript’s format

All of the text should be single spaced with one-inch margins on the left and right sides. Once the text of the manuscript is completed in Word, convert the Summary through Discussion sections from a single column format to double column format. Select these sections of the text, click on “Format” heading, then “Columns” from the drop-down menu. Select two columns and equal column width and then change spacing to 0.25 inches. Title and running title sections as well as references, footnotes, figure legends and table s should remain in single column format.

Use Times New Roman font and select size and bolding to mimic the appearance shown above for the title section; use 11 point for the remaining text.

Do not imbed graphics in the Word document but add them at the end of the PDF as described below.

2. Prepare figures at publication quality resolution, using only applications capable of generating high resolution TIFF or EPS files. Number each figure. For important requirements information on the preparation of figures, go to http://art.cadmus.com/da/jbc/index.jsp. Rapid Inspector is now available for use by authors. The Rapid Inspector software allows authors to check their figure files against JBC standards for format, resolution, color space and other figure requirements. Click here to download Rapid Inspector to your computer.

3. Using Adobe Acrobat (see http://adobe.com/products/main.html for information), save your manuscript text and figures in a single file in PDF format with the figures at the end. The file name should be one word with no spaces and a .pdf extension at the end ( e.g. manuscript.pdf ). Authors are responsible for assuring the accuracy and quality of the PDF. Please consult your Adobe Acrobat manual for instructions regarding PDF file creation.

4. Print the PDF file and carefully review text and figures. It is the author’s responsibility to assure that the manuscript is suitable for review, particularly figures. Manuscripts that do not have figures of sufficient quality for scientific review will be returned to authors. Check the PDF file size. Most files should be around 1 MB, but not larger than 5 MB. If the file is larger than 5 MB, you may adjust the default settings of Adobe Acrobat to create a smaller size file. We will not process your submission if your PDF is larger than 5 MB. If you need help, please contact the JBC office at jbc@asbmb.org

5. Submit your manuscript at http://www.jbc.org/submit. You will need:

- Contact information for the Submitting Author
- Information about the authors and the manuscript
- A cover letter with information for the Editor and Associate Editors
- Single PDF file of your manuscript under 5 MB in size. This file should contain text and figures.

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## Revised Manuscript Submission

Revised manuscripts are prepared exactly as described above for initial submission and submitted via the JBC submission system at http://www.jbc.org/submit. Responses to raised concerns should be transmitted in the cover letter, not in the PDF file containing the manuscript.

## Accelerated Publication Submission

Accelerated Publications are intended to present new information of exceptional novelty, importance and interest to the broad readership of the JOURNAL. Accelerated Publications must be five printed pages or less, including all figures, references and tables. A standard 5 page paper contains 30,000 characters, including spaces, plus 2 tables or figures. They are not intended simply to be short versions of Regular Papers. Because the criteria for acceptance of Accelerated Publications are considerably more stringent and the review process is expedited, an Associate Editor may judge a manuscript unsuitable without obtaining a full review.

## Final Submission of an Accepted Manuscript

If your manuscript is accepted for publication by JBC, the final PDF version will be published as a JBC Papers in Press within 24 hours of acceptance.

You are then required to send the final version as source files including a separate Word file for text and graphic TIFF and EPS files for the figures directly to Cadmus Professional Communications via their FTP site. Specific instructions will follow acceptance of the manuscript. These files must be exactly the same files from which the final PDF was prepared; otherwise they will be rejected, delaying publication.

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# Organization of the Manuscript

1. Formatted for 8.5 x 11 inch paper
2. Single spacing throughout
3. Two column page format including Summary through Discussion sections. Title section as well as references, footnotes, figure legends and tables at the end of the manuscript are in single column format. Click here to see an example.
4. One-inch left and right margins and 0.25 inch spacing between columns.
5. Text typed in Times New Roman, 11 point
6. Manuscript is to be arranged in the following order:

(a) title, author(s), and complete name(s) of institution(s) and running title
(b) summary
(c) introduction
(d) experimental procedures
(e) results
(f) discussion
(g) references
(h) footnotes
(i) figure legends
(j) tables
(k) figures
(l) supplemental data ( if applicable )

7. Number all pages including figures. Please note: Any paper submitted without page numbers will be deleted and you will be asked to resubmit with pages numbers using the online submission system.

## TEXT

Title Section

· Title - as short and informative as possible, should not contain non-standard acronyms or abbreviations and should not exceed two printed lines

· Authors - contains names of all authors and their complete mailing addresses and identifies who will receive all correspondence regarding the manuscript, including proofs:

a) name
b) telephone and fax numbers
c) email address

· Running Title - will be at the top of each printed page and cannot exceed 60 characters and spaces

· Summary

- should succinctly and clearly describe the major findings reported in the manuscript
- must not exceed 250 words nor contain abbreviations or specialized terms
- should be understandable in itself, since it is frequently used as an abstract

· Introduction

- presents the purpose of the studies reported and their relationship to earlier work in the field
- should not be an extensive review of the literature nor, in general, exceed one typed page

· Experimental Procedures

- brief but sufficiently complete to permit a qualified reader to repeat the experiments reported
- only truly new procedures should be described in detail
- cite previously published procedures in References
- modifications of previously published procedures not given in detail except when necessary to repeat the work

· Results

- presented in figures and tables
- some results not requiring documentation given solely in the text
- extensive discussion not in Results section

· Discussion

- concise (usually less than two typed pages)
- focused on the interpretation of the results rather than a repetition of the Results section

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## References

- cited in text by number rather than author and date
- numbered consecutively in the order of appearance in the manuscript
- References for journals and books should be in the following styles:

1. MacDonald, G. M., Steenhuis, J. J., and Barry, B. A. (1995) J. Biol. Chem. 270, 8420-8428

2. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring HarborLaboratory, Cold Spring Harbor, NY

Journal names are abbreviated according to Chemical Abstracts (http://www.cas.org/). Authors are fully responsible for the accuracy of the references.

Miscellaneous

· Footnotes are used to cite manuscripts in preparation, unpublished observations, and personal communications. Authors are responsible for obtaining written approval for all personal communications and sending a copy of the manuscript to those cited. The Editor may request proof of such approval.

· All abbreviations used in the text must be defined in a single footnote inserted in the text immediately after the first abbreviation is cited. The abbreviations of some important biochemical compounds, e.g. ATP, NADH, DNA, and amino acids in proteins, need not be defined. Phrases such as "central nervous system" or "red blood cells" should not be abbreviated. Names of enzymes are usually not abbreviated except in terms of the substrates for which there are accepted abbreviations, e.g. ATPase and RNase.

· The trivial and systematic names of enzymes should be those recommended by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) in "Enzyme Nomenclature, Recommendations, 1992" (1992, Academic Press).

· Notes added in proof to a manuscript only with the consent of the Associate Editor

· Errors in a published paper will be corrected in the J OURNAL in "Additions and Corrections"

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## Tables and Figures

The number of tables and figures used to present data essential to illustrate or prove a point should be kept to a minimum. Very complex or large tables should be submitted as a figure or as a supplement to JBC On-line. For example, amino acid or nucleic acid sequences with alignments. It is also possible to submit complex data that is difficult to print as a supplement to JBC On-line (see below).

Tables should have titles and sufficient experimental detail in a legend immediately following the title to be understandable without reference to the text. Each column in a table must have a heading, and abbreviations, when necessary, should be defined in the legend.

Figures should have titles and explanatory legends containing sufficient detail to make the figure easily understood. All legends should be printed consecutively in a separate section of the manuscript. Authors are responsible for providing digital art that has been properly sized and cropped. Appropriately sized numbers, letters, and symbols should be used so they are no smaller than 2 mm in size after reduction to a single column width (20 picas, 8.7 cm, 3.25 inches), a 1.5-column width (29 picas, 12.0 cm, 4.75 inches), or a full 2-column width (42 picas, 17.8 cm, 7 inches). Superscript and subscript characters are not excluded from this rule. Numbers, letters, and symbols used in multi-paneled figures must be consistent. The abscissa and ordinate should be clearly labeled with appropriately sized type, and units of measurement must be given. Failure to comply with these specifications will require new figures and delay publication. Scales for plotting the data should be marked by short index lines, but every index line need not be numbered. Use standard symbols found in MS Word with symbols and curves identified in the legend and not on the figure. Indicate the figure number on the front of each figure.

All figures should be created with applications that are capable of preparing high resolution TIFF or EPS files acceptable for publication. Although you will initially submit figures with the text in a single PDF file, we will require submission of figures as separate TIFF or EPS files at publication quality resolution for print and online publication if your paper is accepted. For important information on the preparation of figures in TIFF or EPS, go to http://art.cadmus.com/da/jbc/index.jsp. The list of acceptable graphic Mac OS and Microsoft Windows applications may be found at http://art.cadmus.com/da/jbc/applications.jsp. These applications can be used to successfully create high quality TIFF and EPS files and you will find instructions on how to save them properly at this URL. Because more applications are added as testing continues, please review this list periodically. It is the author's responsibility to verify the quality of the graphics in the PDF that has been prepared and that compression of the files for submission does not distort the images.

While image manipulation is often desirable for clarity and/or brevity of presentation, manipulation for deceptive purposes either to unfairly enhance or eliminate or otherwise obscure data is misconduct and will be resolved according to Journal policy.

For graphic material, we have adopted a policy taken from The Journal of Cell Biology.

“No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The groupings of images from different parts of the same gel, or from different gels, fields or exposures must be made explicit by the arrangement of the figure (e.g. using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if and as long as they do not obscure or eliminate any information present in the original. Nonlinear adjustments (e.g. changes to gamma settings) must be disclosed in the figure legend.”

Please be aware of several key issues when preparing graphics for publication:

1. The JBC is now in an RGB (Red, Green, Blue) workflow for color figures. Prior to June 1, 2005, authors were required to submit figures in CMYK (Cyan, Magenta, Yellow, blacK) color mode, as this is the native color mode for the printing process and thus optimizes color for press. As of June 1 2005, all color figures should be submitted in RGB format. Images supplied by authors in RGB color will retain the brilliant reds, greens, and blues for online publication, but may experience a color shift in printed form. To learn more, please see http://art.cadmus.com/da/jbc/index.jsp

2. Images supplied in EPS format should have all fonts converted to outlines/paths. If fonts are not converted to paths or outlines, there is a possibility of character substitutions or that your graphic may have to be converted to a bitmap, which can affect online image quality. The following screenshot demonstrates how to convert fonts to outlines/paths in Adobe Illustrator:

3. Excessive file compression for submission can distort images so that PDFs should be carefully checked.

4. Images containing both greyscale and bitmap areas must be supplied at a minimum resolution of 600 dpi. If possible, it is best to prepare such images as vector files for the line art areas, with embedded TIFF images for the greyscale portions.

5. We cannot accept figure files in certain applications such as Microsoft Office (PowerPoint, Word, Excel, Access), Corel Perfect Office (WordPerfect, Quattro Pro, Presentations), Lotus SmartSuite (Freelance Graphics, 1-2-3, Approach, and WordPro). They are not intended for high resolution imaging necessary for publication. For example, problems with PowerPoint that impact both the visual quality and accuracy of print reproduction include:

- Poor Color Reproduction - PowerPoint files are intended for screen display (RGB color model) and must be color separated for creation of printing plates involving transformation to CMYK color (commercial printing). Colors that are represented in a PowerPoint presentation may not be possible to reproduce on printing.

- Lack of resolution control - Because PowerPoint is intended for screen displays rather than print production; it does not offer full control over resolution. Lettering and other figure parts may appear jagged.

- Poor Font Management - If a computer does not have a font in a PowerPoint presentation created on another computer, it will substitute the font (usually with nonsense) without warning.

To learn how to convert PowerPoint images to an acceptable format for publication, please see: https://rapidsubmission.cadmus.com/jbc/JBC%20PowerPoint%20Update.pdf

Below are examples of a good quality figure and a poor quality figure. The good quality figure has all the wording on the figure in proportion whereas the poor quality figure has a wide variety of lettering sizes.

Bad Quality Figure | Good Quality Figure

After a manuscript is judged acceptable for publication by JBC the figure TIFF and EPS files as well as the Word text file will be submitted online at a FTP site maintained by Cadmus Professional Communications. Specific instructions will follow acceptance of the manuscript.

There will be a charge of $25 per figure for publication of halftone figures. We encourage authors to use color figures when they will enhance the presentation of the data. The cost is $300 for each illustration containing color. (Note: When using the electronic submission system, any figure submitted in color will be reviewed and processed with the understanding that the figure will be published in color.)

If you require further information, please send an email query to jbc@asbmb.org

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## Supplemental Data

The JBC On-line provides the opportunity for authors to include data impossible or impractical to include in the printed J OURNAL. We feel that the ability to include such data in JBC On-line will substantially enhance an author's ability to communicate important research information and will also greatly benefit readers.

We strongly encourage authors to include data such as videos, 3-D structures/images, sequence alignments, and data sets that are very large such as those obtained with microarray hybridization experiments. These data will be reviewed as a part of the normal manuscript review process and will be judged by the same criteria. Only data that are uniquely suited to the On-line journal and which substantially contribute to the manuscript will be accepted. Data files can be prepared in Plain Text, MS Word, HTML Page, MS Excel, TIFF, JPEG or GIF. When practical supplemental data files should be converted and submitted as PDF files. Movies and large excel files should be submitted in their native formats.

Videos should be submitted as QuickTime Video, MPEG movie or MS AVI video and may be prepared on either a PC or Mac computer. All videos should be submitted at the desired reproduction size and length. To avoid excessive delays in downloading the files, videos should be no more than 5 MB in size and 30 and 60 seconds in length. Authors are encouraged to use QuickTime's "compress" option when preparing files to help control file size. Additionally, cropping frames and image sizes can significantly reduce file sizes. Files submitted can be looped to play more than once, provided file size does not become excessive. Authors will be notified if problems exist with videos as submitted and will be asked to modify them. No editing will be done to the videos at the editorial office. All changes are the responsibility of the author.

File name(s) should be one word with no spaces and the appropriate extension at the end. ( e.g. movie1.mov, movie2.qt, table1.xls ).

IMPORTANT: One traditional still image of the author's choosing must be submitted per video. This image will be published to act as a link from the text to the full video file. It will also appear in the text of the printed journal in place of the video. Please indicate clearly in your text whether a figure has a video associated with it and be sure to indicate the name of the corresponding video file. A brief figure legend should also be provided. The figures should be prepared using the guidelines for figures indicated earlier in these instructions. For more information regarding the submission of videos, please contact the JBC editorial office.

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## Publication Charges

> Page Charges -- $75 per journal page
> Color Figures -- We encourage authors to use color figures when they will enhance the presentation of the data. The cost is $300 for each illustration containing color. (Note: When using the electronic submission system, any figure submitted in color will be reviewed and processed with the understanding that the figure will be published in color.)
> Halftones -- $25 per figure
> Reprints – Pricing is based on quantity ordered.

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# Chemical and Mathematical Usage

Table I lists the abbreviations for units of measurement and certain physical and chemical quantities used by the J OURNAL without definition. Also listed are the prefixes that can be added to names of units and the multipliers indicated by each prefix.

View this table: [in this window] | Table I Abbreviations of units of measurement and of physical and chemical quantities (These abbreviations may be used without definition. They are not followed by periods. The same form is used in the plural.) The J OURNAL recommends the use of the International System of Units (SI) (Page, C. H., and Vigoureux, P., Editors, NBS Special Publication 330, U.S. Government Printing Office; see also the IUPAC Manual of Symbols and Terminology for Physicochemical Quantities and Units (1979) Pergamon Press). However, it will continue to accept certain units as listed here (e.g. angstrom, calorie, minute) even though they are not part of the SI. Note that wavelength should be expressed in nanometers or in angstrom units; millimicron is specifically unacceptable.

Chemical equations, structural formulas, and mathematical equations should be placed between successive lines of text. In general, the rules and recommendations of the IUBMB and the International Union of Pure and Applied Chemistry (IUPAC) will be used for abbreviation of chemical names, nomenclature of chemical compounds, enzyme nomenclature, isotopic compounds, optically active isomers, and spectroscopic data. We recommend the use of the classification, nomenclature, and structural representation of lipids used by the LIPID MAPS Initiative (see Fahy et al. J. Lipid Res. 2005 46: 839-862). You can download lipid structures directly from the LIPID MAPS Structure Database (http://www.lipidmaps.org). This database draws structures de novo, allowing you to insert them into your documents. Table II lists references to publications of the rules and recommendations of the International Scientific Unions that may be consulted for detailed information.

View this table: [in this window] | Table II Tentative Rules and Recommendations of International Scientific Unions Many of the documents in this table can be obtained on the internet at http://www.chem.qmw.ac.uk/iupac/index.html.

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# Protein and Nucleic Acid Sequences

Newly reported nucleotide or protein sequences must be deposited in GenBank or EMBL databases, and an accession number must be obtained BEFORE the paper is accepted by the Associate Editor. Access to the information in the database must be available at the time of publication. Authors are responsible for arranging release of data at the time of publication. The authors must also provide a statement in the manuscript that this sequence has been scanned against the database and all sequences with significant relatedness to the new sequence identified (and their accession numbers included).

Authors of accepted papers containing nucleotide sequences must submit the sequence data, preferably in computer-readable form or by electronic mail, and a copy of the paper to either:

GenBank

> GenBank Submissions
> National Center for Biotechnology Information
> 8600 Rockville Pike, Building 38A
> Room 8N-805
> Bethesda, MD 20894
> Tel: (301) 496-2475
> On the web at: http://www.ncbi.nlm.nih.gov/Genbank/index.html

Or

EMBL Nucleotide Sequence Submissions

> European Bioinformatics Institute,
> Hinxton Hall,
> Hinxton, Cambridge CB10 1SD, UK
> Tel.: 44-1223-494401; Fax: 44-1223-494472
> e-mail: support@ebi.ac.uk
> On the web at: http://www.ebi.ac.uk

Or

DNA Data Bank of Japan

> Center for Information Biology
> National Institute of Genetics
> Mishima, Shizuoka, 411, Japan
> Tel.: 81-559-81-6853; Fax: 81-559-81-6849
> On the web at: http://www.ddbj.nig.ac.jp

A footnote will be included in the paper indicating that such a deposit has been made. Submission to any data bank is sufficient to ensure entry in all. When nucleotide probes are used, the ends of the probes should be explicitly identified by reference to published nucleotide number or restriction maps, or, if unpublished, the information should be included in the Experimental Procedures section.

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# Genomic and Proteomic Studies

Authors of papers that include genomic, proteomic, or other high-throughput data are required to submit their data to the NCBI gene expression and hybridization array data repository (GEO, http://www.ncbi.nlm.nih.gov/geo/) and to provide the GEO accession number. The data must be submitted and an accession number obtained BEFORE the Associate Editor accepts the paper. Release of the information in the database must be available at the time of acceptance because they are published immediately as papers in press.Access to the information in the database must be available at the time of publication.

GEO has a web-based submission route, suitable for a small number of samples, or a batch submission tool (called SOFT). GEO is accessible from http://www.ncbi.nlm.nih.gov/geo/. Submission FAQ is at: http://www.ncbi.nlm.nih.gov/geo/info/general_faq.cgi.

Submitted data is encouraged to follow the MIAME checklist (for more information see http://www.mged.org/Workgroups/MIAME/miame_checklist.html).

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# Structural Studies

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), MSD-EBI (www.ebi.ac.uk/msd), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu). The PDB ID should be included in the manuscript. 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 info@wwpdb.org.
Authors must supply all information BEFORE the paper is accepted by the Associate Editor. After completion of the editorial process, the manuscript will not be accepted until confirmation has been received from the author, if not initially supplied, that the required information has been deposited and will be available BEFORE acceptance. No data is to be withdrawn from PDB once a paper has been accepted and published as a Papers in Press (PIP) article.

As of 12/06, PDB no longer accepts coordinates for model structures determined by computational methods. The coordinates must be included as a supplement to the online paper and formatted just as if it were a PDB submission.
Click here for additional guidelines

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# Database Accession Hyperlinks For JBC On-line

The electronic version of the J OURNAL employs direct hyperlink access to entries in databases such as GenBank. Authors are required to provide accession numbers to databases for all newly described molecular structures reported in their manuscripts.

In addition, authors are strongly encouraged to include accession numbers for any database information that would aid a reader in understanding the authors' paper regardless of who had deposited the database information.

In order for the database hyperlinks to be generated, the citation must appear as a Footnote and be written exactly as follows:

1. GenBank = GenBank Accession Number XYYYYY
2. Molecular Modeling Database = MMDB # XYYY
3. NCBI Protein Database = NCB Accession # XXXXX
4. Swiss Protein Database = Swiss-Prot # XXXX
5. Enzyme Collection Number = xx.yy.zz.bb
6. Research Collaboratory for Structural Bioinformatics Protein Databank = PDB # XXXX

The molecule or structure for an accession number can be identified through the NCBI Entrez utility at http://www.ncbi.nlm.nih.gov/Entrez/.

The following shows how references to databases should be written in a footnote.
"The nucleotide sequence for the artificial sperm whale myoglobin gene has been deposited in the GenBank database under GenBankAccession Number (Reference). The amino acid sequence of this protein can be accessed through NCBI Protein Database under NCBI Accession # 2311060 (Reference). The atomic coordinates for the crystal structure of this protein are available in the Molecular Modeling Database (http://www.nnlm.nlm.nih.gov/mar/molbio/3D/index.htm) under MMDB # 5MBN(Reference)."

Authors may include their email address and home page URL. However, authors cannot cite in the manuscript that additional data not presented in the manuscript are available at the homepage. Home page URLs will not be hyperlinked.

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