The Open Structural Biology Journal

ISSN: 1874-1991 - Volume 4, 2010

Instructions for Authors

The Open Structural Biology Journal is an Open Access online journal, which publishes Research articles, Reviews and Letters in the field of structural biology, aiming at providing the most complete and reliable source of information on current developments in the field.

Manuscripts may be submitted directly to tosbj@benthamopen.org. Each peer-reviewed article that is published in a Bentham OPEN Journal is universally and freely accessible via the Internet in an easily readable and printable PDF format.

ONLINE MANUSCRIPT SUBMISSION: An online submission and tracking service via Internet facilitates a speedy and cost-effective submission of manuscripts.¹ The full manuscript has to be submitted online via Bentham's Content Management System (CMS) at http://www.bentham-editorial.org/ View Instructions

Alternatively, you may also submit your full manuscript by e-mail to tosbj@benthamopen.org

Manuscripts must be submitted by one of the authors of the manuscript, and should not be submitted by anyone on their behalf. The principal/corresponding author will be required to submit a Covering Letter along with the manuscript, on behalf of all the co-authors (if any). The author(s) will confirm that the manuscript (or any part of it) has not been published previously or is not under consideration for publication elsewhere. Furthermore, any illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained.

For all online submissions, please provide your complete manuscript in the form of a single zipped folder containing soft copies of all the materials (main text in MS Word or Tex/LaTeX), figures/illustrations in TIFF, PDF or JPEG, and chemical structures drawn in ChemDraw (CDX)/ISISDraw (TGF) as separate files, while a PDF version of the entire manuscript must also be included, embedded with all the figures/illustrations/tables/chemical structures etc.

A successful electronic submission of a manuscript will be followed by a system-generated acknowledgement to the principal/corresponding author within 72 hours of the dispatch of the manuscript. Any questions with regards to the preparation of and submission of your manuscript to the journal should be addressed to tosbj@benthamopen.org and copied to atifa@benthamscience.org

NOTE: Any queries therein should be addressed to oa@bentham.org and copied to Jalil@bentham.org

Manuscript Preparation: The manuscript should be written in English in a clear, direct and active style. All pages must be numbered sequentially, facilitating in the reviewing and editing of the manuscript.

For further convenience, the customer support team available at Bentham Publishing Services (www.benthampublishingservices.com) can provide assistance to authors for the preparation of manuscripts.

Manuscript Length:

Letters: The maximum total page length for Letter type articles published in the journal is nine journal pages. Each journal page is on average 900 words.

Research Articles: The minimum total page length for Research articles is ten journal pages, and the maximum thirty pages. Each journal page is on average 900 words.

Review Articles: The maximum page length limit for comprehensive Review articles is forty pages. For Mini-Review articles, the maximum page length is nine journal pages. Each journal page is on average 900 words.

There is no restriction on the number of figures, tables or additional files e.g. video clips, animation and datasets, that can be included with each article online. Authors should include all relevant supporting data with each article.

Manuscripts Published: The Journal accepts letters/short communications, original research articles, and mini- and full-length review articles written in English. Supplements, proceedings of conferences and book reviews may also be considered for publication.

Supplements/Single Topic Issues: The journal also considers Supplements/Single topic issues for publication. A Supplements/Single topic will be a collection of articles (minimum of 6, maximum of 20 articles) based on a contemporary theme or topic of great importance to the field. Mini-supplements consisting of between 3 to 5 articles are also welcome. A Supplement can consist of either all review articles or a mixture of review and research articles. The Guest Editors' main editorial task is to invite the contributors to the Supplement and to manage the peer review of submitted manuscripts. A short summary or proposal for editing a supplement should be submitted to the Editor-in-Chief at e-mail to tosbj@benthamopen.org with a copy to specialissue@benthamopen.org

Conference Proceedings: The journal will consider for publication proceedings of relevant conferences in the field. Proposals for publishing conference proceedings should be submitted to the Editor at e-mail tosbj@benthamopen.org with a copy to oa@bentham.org

Open Access Book Reviews: This journal publishes open access reviews on recently published books (both print and electronic) relevant to the journal. Publishers and authors of books are invited to contact our book reviews editor at tosbj@benthamopen.org with book review requests. All submitted books will be reviewed by an independent expert in the field.

MANUSCRIPT SECTIONS FOR PAPERS: Manuscripts for research articles and letters submitted to the journal should be divided into the following sections; however, there can be an extension in the number of sections in review articles in accordance with the requirements of the topic.

Covering letter
Title page
Abstract
Text organization
List of abbreviations (if any)
Conflict of interest (if any)
Acknowledgements (if any)
References
Appendixes
Figures/illustrations (if any)
Chemical structures (if any)
Tables and captions (if any)
Supportive/supplementary material (if any)

COVERING LETTER: It is a mandatory requirement that a signed covering letter also be submitted along with the manuscript by the author to whom correspondence is to be addressed, delineating the scope of the submitted article declaring the potential competing interests, acknowledging contributions from authors and funding agencies, and certifying that the paper is prepared according to the 'Instructions for Authors'. All inconsistencies in the text and in the reference section, and any typographical errors must be carefully checked and corrected before the submission of the manuscript. The article contains no such material or information that may be unlawful, defamatory, fabricated, plagiarized, or which would, if published, in any way whatsoever, violate the terms and conditions as laid down in the agreement. The authors acknowledge that the publishers have the legal right to take appropriate action against the authors for any such violation of the terms and conditions as laid down in the agreement. Download the Covering letter

TITLE: The title should be precise and brief and must not be more than 120 characters. Authors should avoid the use of non standard abbreviations. The title must be written in title case except for articles, conjunctions and prepositions.

Authors should also provide a short ‘running title’.

ABSTRACT: The abstract should not exceed 250 words for review and research papers and should be limited to only 150 words for letters, summarizing the essential features of the article. The use of abbreviations should be reduced to a minimum and the references should not be cited in the abstract.

TEXT ORGANIZATION: The main text should begin on a separate page and should be divided into separate sections. For Research articles, the preparation of the main text must be structured into separate sections as Introduction, Materials and Methodology, Results, Discussion and Conclusion. For Review and Letter articles, the manuscript should be divided into title page, abstract and the main text. The text may be subdivided further according to the areas to be discussed, which should be followed by the Acknowledgement (if any) and Reference sections. The review article should mention any previous important reviews in the field and contain a comprehensive discussion starting with the general background of the field. It should then go on to discuss the salient features of recent developments. The authors should avoid presenting material which has already been published in a previous review. The manuscript style must be uniform throughout the text and 10 pt Times New Roman font should be used. The full term for an abbreviation should precede its first appearance in the text unless it is a standard unit of measurement. The reference numbers should be given in square brackets in the text. Italics should be used for Binomial names of organisms (Genus and Species), for emphasis and for unfamiliar words or phrases. Non-assimilated words from Latin or other languages should also be italicized e.g. in vivo, in vitro, per se, et al. etc. Protein and Nucleic acid sequences may be included and should conform to International databases. Genomic and Proteomic studies may be included and should conform to International databases.

It is advisable that the observations be presented and discussed in brief. Make available all products that they generate such as protein, DNA, clone, cell or other types of material that they describe to other investigators in the field who require them for bona fide purposes. This should be done with the spirit that the data that are published can be duplicated and that other ideas can be tested. For research involving human subjects, authors must name the committee(s) that approved the experiments in the Materials and methods section of the paper and include with their submission a statement to confirm that informed consent was obtained from all subjects.

MICROARRAY DATA: The authors will be required to submit the Microarray experiment data to the ArrayExpress using the MIAMExpress submission tool (www.ebi.ac.uk/miamexpress), which will be subjected to reviewing by the curation team and if accepted, an ArrayExpress accession number would be assigned for it. The ArrayExpress offers the facility to maintain the data until the related paper is published.

Microarray data should be made available for reviewers and editors at the time of manuscript submission in a MIAME compliant and widely accessible format. Submission of large raw and/or analyzed microarray data files as supplementary data to the journal should be discouraged, which may alternatively be submitted either to the Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ or ArrayExpress http://www.ebi.ac.uk/arrayexpress repositories, thereby obtaining an accession number for the journal and any necessary passwords, to facilitate the reviewers and editors of a manuscript to access the data. The submission of the microarray data to either of these repositories should be done at or before acceptance of a paper for publication, with accession number being allotted well before publication.

Nomenclature:

The authors are encouraged to use standardized nomenclature wherever necessary:

•The SI units should be used; if not exclusively, please provide the SI value in parentheses after each value.
•Species names should be italicized (e.g., Homo sapiens). The generic name of a species should be given in full the first time it appears in the text.
The author authority for each species is desirable on its first mention.
Chemical formulae may not be used as abbreviations in the text.
•Genes, mutations, genotypes, and alleles should also be indicated in italics but the protein product of a gene should be in Roman type. Use the recommended name by consulting the appropriate genetic nomenclature database, e.g., HUGO for human genes. It is sometimes advisable to indicate the synonyms for the gene the first time it appears in the text. Gene prefixes such as those used for oncogenes or cellular localization should be shown in roman: v-fes, c-MYC, etc.
•The Recommended International Non-Proprietary Name (rINN) of drugs should be provided.
•In case of usage of symbols that do not conform to those that have previously appeared in the literature, their aliases may be obtained from the approved nomenclature in the HGNC (HUGO Gene Nomenclature Committee) [http://www.genenames.org/] and LocusLink, to allow retrieval of all the information available for each gene.

Taxonomic nomenclature: The Latin name and taxonomic authority (e.g. Linnaeus) should be given for all experimental species. Chemical nomenclature must conform to the Subject Index of Chemical Abstracts.

Accession Numbers:

All appropriate datasets, images, and information should be deposited in public resources. Please provide the relevant accession numbers (and version numbers, if appropriate) and any necessary passwords to enable the reviewers and editors of a manuscript to access the data.

Providing accession numbers facilitates linking to and from the established databases and integrates the article with a broader collection of scientific information, therefore list all accession numbers should be listed directly after the Supporting Information section.

All accession numbers for all entities such as genes, proteins, mutants, diseases, etc., for which there is an entry in a public database should be included in the manuscript. Experimental data should be submitted to the appropriate databases, with a release date corresponding to the date of publication.

Greek Symbols and Special Characters: Greek symbols and special characters often undergo formatting changes and get corrupted or lost during preparation of manuscript for publication. To ensure that all special characters used are embedded in the text, these special characters should be inserted as a symbol but should not be a result of any format styling (Symbol font face) otherwise they will be lost during conversion to PDF/XML².

Authors are encouraged to consult reporting guidelines. These guidelines provide a set of recommendations comprising a list of items relevant to their specific research design. All kinds of measurements should be reported only in International System of Units (SI).

LIST OF ABBREVIATIONS: Abbreviations use should be restricted to a minimum. All non-standard abbreviations should be listed in alphabetical order, along with their expanded form, defining them upon the first use in the text. Non-standard abbreviations should not be used unless they appear at least three times in the text. If abbreviations are used in the text either they should be defined in the text where first used, or a list of abbreviations can be provided.

CONFLICT OF INTEREST: Financial contributions to the work being reported should be clearly acknowledged, as should any potential conflict of interest.

ACKNOWLEDGEMENTS: Please acknowledge anyone (individual/company/institution) who has contributed to the study by making substantial contributions to conception, design, acquisition of data, or analysis and interpretation of data, or who was involved in drafting the manuscript or revising it critically for important intellectual content. Please list the source(s) of funding for the study, for each author, and for the manuscript preparation in the acknowledgements section.

This journal complies with the International Committee of Medical Journal Editors' Uniform Requirements for Manuscripts Submitted to Biomedical Journals www.icmje.org and the FDA's Good Reprint Practices for the Distribution of Medical Journal Articles and Medical or Scientific Reference Publications on Unapproved New Uses of Approved Drugs and Approved or Cleared Medical Devices http://www.fda.gov/oc/op/goodreprint.html

REFERENCES: References must be listed in the numerical system (Vancouver). All references should be numbered sequentially [in square brackets] in the text and listed in the same numerical order in the reference section. The reference numbers must be finalized and the bibliography must be fully formatted before submission.

See below few examples of references listed in the correct Vancouver style:

Typical Paper Reference:
[1] Lu M, Taylor A, Chylack LT, et al. Dietary linolenic Acid intake is positively associated with five-year change in eye lens nuclear density. J Am Coll Nutr 2007; 26: 133-40.
[2] Nocentini G, Ronchetti S, Cuzzocrea S, Riccardi C. GITR/GITRL: more than an effector T cell co-stimulatory system. Eur J Immunol. 2007; 37: 1165-9.

Typical Chapter Reference:
[3], Siegal BS, Chiu CJ, Taylor A. In: Bendich A, Deckelbaum RJ, Eds. Preventive Nutrition 3/e. Totawa, NJ, Humana Press 2005; 463-503.

Book Reference:
[4] Carlson BM. Human embryology and developmental biology. 3rd ed. St. Louis: Mosby; 2004.

Edited Book:
[5] Brown AM, Stubbs DW, Eds. Medical physiology. New York: Wiley; 1983.

Conference Paper:
[6] Anderson JC. Current status of chorion villus biopsy. In: Tudenhope D, Chenoweth J, Eds. Proceedings of the 4th Congress of the Australian Perinatal Society; 1986: Brisbane, Queensland: Australian Perinatal Society; 1987; pp. 190-6.

Conference Proceedings:
[7] Harris AH, Ed. Economics and health: 1997: Proceedings of the 19th Australian Conference of Health Economists; 1997 Sep 13-14; Sydney, Australia. Kensington, N.S.W.: School of Health Services Management, University of New South Wales; 1998.

Journal Article on the Internet:
[8] Andrew DB, Gregory YHL. Venous thromboembolism. BMJ [serial on the Internet]. 2006 Jan; [cited 2006 January 28]; 332: [about 10 screens]. Available from: http://www.bmj.com/cgi/content/full/332/7535/215

Book/Monograph on the Internet:
[9] Donaldson MS, Ed. Measuring the quality of health care [monograph on the internet]. Washington: National Academy Press; 1999 [cited 2004 Oct 8]. Available from: http://legacy.netlibrary.com/

Website/Homepage:
[10] HeartCentreOnline [homepage on the Internet]. Boca Raton, FL: HeartCentreOnline, Inc.; c2000-2004 [updated 2004 May 23; cited 2004 Oct 15]. Available from: http://www.heartcenteronline.com/

Journal with Part/Supplement:
If a journal carries continuous pagination throughout the volume, then the issue number can be omitted.

Issue with Supplement:
[11] Glauser TA. Integrating clinical trial data into clinical practice. Neurology 2002; 58(12 Suppl 7): S6-12.

Volume with Part:
[12] Abend SM, Kulish N. The psychoanalytic method from an epistemological viewpoint. Int J Psychoanal 2002; 83(Pt 2): 491-5.

Issue with Part:
[13] Ahrar K, Madoff DC, Gupta S, Wallace MJ, Price RE, Wright KC. Development of a large animal model for lung tumors. J Vasc Interv Radiol 2002; 13(9 Pt 1): 923-8.

Patent:
[14] Alison AM, Daniel T, Stephen JR, John AL, Thomas HT, inventors; Large Scale Biology Corporation, assignee. Self antigen vaccines for treating B cell lymphomas and other cancers. United States patent US 7084256. 2006 Aug.

E-citations:
[15] Citations for articles/material published exclusively online or in open access (free-to-view) , must contain the exact Web addresses (URLs) at the end of the reference(s), except those posted on an author’s Web site unless editorially essential, e.g. ‘Reference: Available from: URL’.

Some important points to remember:

*All references must be complete and accurate.
*If the number of authors exceeds six then et al. will be used after three names (the term “et al.” should be in italics).
*Online citations should include the date of access.
*Journal abbreviations should follow the Index Medicus/MEDLINE.
*Take special care of the punctuation convention as described in the above-mentioned examples.
*Avoid using superscript in the in-text citations and reference section.
*Abstracts, unpublished data and personal communications (which can only be included if prior permission has been obtained) should not be given in the reference section but they may be mentioned in the text and details provided as footnotes.
*The authors are encouraged to use a recent version of EndNote (version 5 and above) or Reference Manager (version 10) when formatting their reference list, as this allows references to be automatically extracted.

APPENDIXES: In case there is a need to present lengthy, but essential methodological details, use appendixes, which can be a part of the article. An appendix must not exceed three pages (Times New Roman, 12 point fonts, 900 max. words per page).The information should be provided in a condensed form, ruling out the need of full sentences. A single appendix should be titled APPENDIX, while more than one can be titled APPENDIX A, APPENDIX B, and so on.

FIGURES/ILLUSTRATIONS: The authors should provide the illustrations as separate files, as well as embedded in the text file, numbered consecutively in the order of their appearance. Each figure should include a single illustration. No charges will be levied on the use of color figures except in the reprints. Each figure should be closely cropped to minimize the amount of white space surrounding the illustration.

If a figure consists of separate parts, it is important that a single composite illustration file be submitted, containing all parts of the figure.

Photographs should be provided with a scale bar if appropriate, as well as high-resolution component files.

Scaling/Resolution:

For Line Art image type, which is generally an image based on lines and text and does not contain tonal or shaded areas, the preferred file format is TIFF or EPS, with colour mode being Monochrome 1-bit or RGB, in a resolution of 900-1200 dpi.

For Halftone image type, which is generally a continuous tone photograph and contains no text, the preferred file format is TIFF, with colour mode being or RGB or Grayscale, with a minimum resolution of 300 dpi.

For Combination image type, which is generally an image containing halftone in addition to text or line art elements, the preferred file format is TIFF, with colour mode being or RGB or Grayscale, in a resolution of 500-900 dpi.

Formats:

For illustrations, the following file formats are acceptable:

• Illustrator
• EPS (preferred format for diagrams)
• PDF (also especially suitable for diagrams)
• PNG (preferred format for photos or images)
• Microsoft Word (version 5 and above; figures must be a single page)
• PowerPoint (figures must be a single page)
• TIFF
• JPEG (conversion should be done using the original file)
• BMP
• CDX (ChemDraw)
• TGF (ISISDraw)

Bentham OPEN does not process figures submitted in GIF format.

If the large size of TIFF or EPS figures acts as an obstacle to online submission, authors may find that conversion to JPEG format before submission results in significantly reduced file size and upload time, while retaining acceptable quality. JPEG is a 'lossy' format, however. In order to maintain acceptable image quality, it is recommended that JPEG files are saved at High or Maximum quality.

Files should not be compressed with tools such as Zipit or Stuffit prior to submission as these tools will in any case produce negligible file-size savings for JPEGs and TIFFs, which are already compressed.

Please do not: