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Instructions to Authors 1. Aims and scope The Journal of Molecular Biology will publish studies
of living organisms or their components at the molecular level. Suitable subject areas include:
(a) Genes:
Expression, replication and recombination, sequence organization and structure, genetics of eukaryotes and prokaryotes.
(b) Viruses and Bacteriophages: Genetics, structure, growth cycle.
(c) Cells and Development: Developmental
biology, organelle structure and function, motility, transport and sorting of macromolecules, energy transfer, growth control.
(d) Proteins, Nucleic Acids and other Biologically Important Macromolecules: Molecular structure, physical chemistry, molecular
engineering, macromolecular assembly and enzymology.
The Journal will not as a rule publish papers which fall
outside the areas defined above.
2. Category and length of papers The Journal of Molecular Biology will
publish Reviews, Communications, and full Articles.Communications are brief papers that make a specific well-documented
point. In general, a Communication should include no more than four figures and tables. The text will be continuous, with technical and
methological detail printed in the legend to the tables and figures. Articles should normally be no longer than 15 printed pages
with no more than 10 figures and four tables. Reviews should be sharply focused and balanced accounts of progress in fields of
interest to the general reader. Reviews should be no longer than 12 printed pages and with no more than 12 figures and tables.
Authorship is normally by invitation: an Editor should be consulted in advance by anyone wishing to submit an unsolicited Review.
The Journal of Molecular Biology discourages authors from submitting multiple manuscripts on closely related topics. Authors
wishing to submit a series of manuscripts intended for simultaneous publication must obtain permission from the editors prior to submitting
the manuscripts.
3. Speed of publication
Decisions on manuscripts will be taken as rapidly as possible. Authors should
expect to have reviewers' comments within approximately 6 weeks. Authors should expect to receive page proofs and comments from the copy
editors within 3 weeks of acceptance. Publication in print ordinarily follows within 4 weeks from receipt of authors corrected proofs. The authors' original files will be published online in as little as 2-5 days following acceptance.
4. Editorial policy
Submission of an article implies that the work described has not been published previously (except in the form of an abstract
or as part of a published lecture or academic thesis), that it is not under consideration for publication elsewhere, that its publication
is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted,
it will not be published elsewhere in the same form, in English or in any other language, without the written consent of the Publisher.
Related manuscripts that are in press or that have been submitted elsewhere must be included with the submission.
Acceptance of papers
for publication in the Journal is at the discretion of the Editors. All manuscripts are reviewed initially by the Editorial
Board and only those papers that meet the scientific and editorial standards of the Journal will be sent for outside review.
Authors should indicate a suitable Editor to whom the paper could be allocated. However, the Journal reserves the right to reallocate
manuscripts to the most appropriate Editor.
In general, Editors will seek advice from two or more expert reviewers about the scientific
content and clarity of presentation of papers. Authors are required to suggest the names, affiliations, and contact information for up
to six individuals who could serve as referees and indicate their specific areas of scientific expertise. Suggested referees should be
established scientists with expertise in the field of the paper. If a revision of the manuscript is required, authors will be provided
with the comments of the reviewers and specific instructions from the Editor handling the manuscript.
Manuscripts requiring minor
revision should be returned to the Editor within 60 days. Revised manuscripts received by the Editor after more than 60 days may be treated
as new submissions. The following specific points are brought to the attention of authors:
(a) Originality. The Board
will reject those papers that it considers reveal no more than minor differences from previously published material.
(b) Methodology
papers. Papers that deal only with new methods and do not contain important new results discovered by means of these methods will
be accepted only when the general applicability and interest of the method are immediately obvious and clearly documented in the manuscript.
Improvements on existing methods will in general be viewed as appropriate to more specialized journals unless it can be shown that they
lead to important new insights that were not accessible with current technologies.
(c) Sequences. Papers describing
new members of a gene family will not ordinarily be accepted unless they contain results of particular importance for studies of evolution
or of the function of the gene. In general, papers describing the cloning and sequencing of new genes will be acceptable only if there
is experimental evidence for the function of the gene.
(d) Structural studies. Communications describing preliminary crystallographic
data (crystallization conditions and diffraction pattern and space group) will, in general, no longer be accepted. Papers of this type
will be considered only if, in the judgement of the Editorial Board, they contain results of exceptional interest and importance. Low-resolution
structural studies will be acceptable only if they have clear biological implications and exhibit features of special interest. Papers
describing structures of mutant proteins are appropriate if the mutations have been successfully designed to provide new insights into
structural principles or biological function. Similar criteria apply to structures of proteins from variant species. In the particular
case of unliganded antibody Fab fragments, papers would not normally be acceptable unless they provide novel structural or biological
insight.
(e) Modeled structures. Papers describing modeled structures will in general be considered only if they provide
novel and important biological insights. The reliability of the model must be clearly documented, including evidence that the expected
accuracy level of the model is consistent with the application that is described. This could be based, for example, on the known success
rate of the modeling procedure at specified levels of sequence identity, or the application of model validation procedures. Validation
of the model through experimental tests is always desirable.
(f) Theory and computer simulation. Papers reporting theoretical
studies should have direct applicability to experimental work in a field normally represented in papers published in JMB or should address
issues of current interest to the broader biological community. As a general rule, all theory papers should deal directly with experimental
data; the papers should provide predictions that are testable experimentally or provide an interpretation of experimental observations.
Papers describing computer simulations are generally acceptable only if they provide new insights of high biological significance or
lead to novel interpretations of experimental data. As is the case for modeled structures, evidence must be provided that the accuracy
level of the method is consistent with the application that is described. This might involve, for example, control simulations on systems
that have been well-characterized experimentally.
(g) Database papers. Papers describing biological or molecular databases
will only be accepted if they report important new results discovered by means of that database or the development of a methodology that
meets criterion (b) above. Authors are advised that the emphasis of such papers, including the title and abstract, must be on the results
discovered or the methodology developed rather than on the construction and availability of the database.
5. Sequence data
Papers dealing with amino acid sequences of proteins or with nucleotide sequences must carry a statement that the data have been deposited
with an appropriate data bank, e.g., the European Molecular Biology Laboratory (EMBL) or GenBank Data Libraries. The data base accession
number must be given at the end of the Materials and Methods section of the manuscript under the separate heading 'Accession numbers'.
For example: Coordinates and structure factors have been deposited in the Protein Data Bank with accession number 2XYZ. Lengthy nucleotide
sequences will be published only if, in the judgement of the Editorial Board, these results are of general interest and importance.
6. Structural data
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 (http://www.wwpdb.org): RCSB PDB (http://www.pdb.org),
MSD-EBI (http://www.ebi.ac.uk/msd), PDBj (http://www.pdbj.org),
or BMRB (http://www.bmrb.wisc.edu). Manuscripts must carry a statement that
coordinates and structure factors (or NMR restraints) have been deposited in the Protein Data Bank. The accession number(s) must be cited
in the manuscript at the end of the Materials and Methods section. Authors must agree to release the atomic coordinates and experimental
data immediately upon publication.
It is increasingly common for coordinates to be deposited in the Protein Data Bank without an
associated publication. Before submission to JMB, authors are expected to search the Protein Data Bank for related structures using one
or more alignment programs and report the outcome. Prior deposition of related coordinates, without an associated publication, does not
necessarily preclude publication in JMB. The primary criteria for publication of a structure in JMB are that it provides novel structural
insights or important new functional and biological insights that are likely to be of general interest.
7. NMR assignments
Tables listing resonance assignments will no longer be published in the Journal but should be supplied as supplementary material
for posting on the Internet on ScienceDirect. Supplementary material must be included with the manuscript submitted for review (see below
for full instructions). Authors are strongly encouraged to deposit assignment data in the BioMagResBank (BMRB; http://www.bmrb.wisc.edu).
8. Cell lines
In keeping with NIH guidelines, the Journal considers it to be good practice for cultured cell lines to
be authenticated. A description of the methods used to authenticate cells should be included in the Materials and Methods section. Authors
are expected to check that cell lines used in their experiments are free from mycoplasma infections.
9. Manuscript style
Manuscripts should be written in English and double spaced throughout (including tables, legends and footnotes) on one side of the page
only. All pages should be numbered serially. The following points should be noted:
(a) Title. Titles should be brief
and informative and should not include non-standard abbreviations. A short running title of not more than 50 characters (including spaces)
suitable for page headings should be included on the title page if the full title is longer than this.
(b) Keyword.
Authors should supply five keywords after the Summary.
(c) Affiliations. The name of the laboratory where the work has
been done should be indicated on the title page. The current address of all authors (if different from the laboratory of origin) should
be indicated. The corresponding author must be identified.
(d) Summary. The Summary should not exceed 300 words and should
be intelligible without reference to the main text. The Summary should not include literature references.
(e) Organisation
of text. The conventions used in current issues of the Journal for headings, references etc. should be used in preparing
manuscripts. Articles are divided into sections in the following order: Introduction; Results; Discussion; Materials and Methods.
Other section headings (e.g., Theory, Results and Discussion) may be used if this improves the clarity of presentation. Communications
should not be divided into sections but should include topic headings where appropriate.
(f) References. References should be
listed at the end of the manuscript. They should be listed in the order in which they appear in the text, tables, and figure legends
and numbered sequentially. When cited in the text, reference numbers should be superscripted. Only papers that have been published or
accepted should be cited in the reference list. The title of the article, the volume number, and first and last pages should be cited.
Journal titles should be abbreviated, e.g.,
1. Sanger, F. & Coulson, A. R. (1975). A rapid method for determining sequences
in DNA by the primed synthesis with DNA polymerase. J. Mol. Biol. 94, 441-448.
2. Goto, Y., Calciano, L. J. & Fink, A. F. (1990).
Acid-induced folding of proteins. Proc. Natl. Acad. Sci. USA 87, 573-577.
Articles in books should include the title of the article,
the name of the book, editor(s), edition number, first and last page numbers, the name and the location of the publisher, e.g.,
3. Hanks, S. K. & Hunter, T. (1995). The eukaryotic protein kinase superfamily. In The Protein Kinase FactsBook: Protein-Serine
Kinases (Hardie, G. & Hanks, S., eds), pp. 747, Academic Press, London.
(g) Internet. Reference to material which
is available on the Internet but has not been published elsewhere should be made in the text only and should not be included in the reference
list.
(h) Abbreviations and symbols. SI units and the system of abbreviations and symbols formulated by the IUPAC-IUB
Combined Commission on Biochemical Nomenclature should be followed. When non-SI units are used, their equivalent SI units should be given.
Genetic names should be described according to the appropriate conventions. Genus and species names should be written in full at first
use and in italics (e.g., Escherichia coli, Caenorhabditis elegans).
(i) Roman numerals. Manuscript titles should not
contain roman numerals as a method of distinguishing between parts, or a sequence of manuscripts.
(j) DNA sequences and GenBank
Accession numbers. Authors wishing to enable other scientists to use the accession numbers cited in their papers via links to these
sources should type this information in the following manner:
For each and every accession number cited in an article,
authors should type the accession number in bold, underlined text. Letters in the accession number should always be capitalised.
(See Example 1 below). This combination of letters and format will enable Elsevier's typesetters to recognise the relevant texts as accession
numbers and add the required link to GenBank's sequences.
Example 1: "GenBank accession nos. AI631510, AI631511, AI632198, and BF223228, a B-cell tumor from a chronic lymphatic leukemia (GenBank accession no. BE675048,
and a T-cell lymphoma (GenBank accession no. AA361117)".
Authors are encouraged to check accession numbers used very carefully. An error in a letter or number can result in a dead link. In the final version of the printed article, the accession number
text will not appear bold or underlined.
In the final version of the electronic copy, the accession number text will
be linked to the appropriate source in the NCBI databases enabling readers to go directly to that source from the article.
10.
Illustrations
Clear illustrations greatly improve the impact and readability of papers. The Journal will reproduce
figures accurately, but cannot correct poorly designed or incorrect illustrations. Please note the following points:
(a) Size. Figures will normally be reduced to single column (80 mm width). When essential for clarity, figures may be published
at double column (165 mm width). The maximum page depth is 240 mm. Please ensure that the figure is legible after reduction to these
sizes. It is a good practice to test the reduction on a photocopier. The Journal will accept figures supplied at actual size
for reproduction. This is particularly helpful for electron micrographs, stereo diagrams and complex half tone figures. However, the Journal reserves the right to change figure sizes as necessary.
(b) Lettering and design of figures. A consistent
font style should be used in all figures. Lettering after reduction should be no smaller than 9 pt (approx 2 mm) and no larger than 10
pt (approx 4 mm). Wide variations in type sizes in lettering is undesirable.
(c) Composite figures. In general, no
more than four sections should appear in a single figure. If more than four sections are required, it is better to create several separate
figures. Label individual sections in composite figures clearly with lower case letters, using (a), (b), (c).
(d) Color.
Color illustrations will be published without charge if both the Editor and the Publisher decide that color is essential for the clarity
of the figure.
(e) Stereo pairs. Stereo pairs should be in divergent (wall-eye) view and should be supplied at the same
size as they are to appear in the Journal. Before submitting figures, authors should check carefully that stereo figures are
correct and give the proper stereo image.
(f) Electronic submission of figures. When artwork is scanned for publication,
a resolution of 1000 dpi is required for line artwork, 300 dpi for halftones (photographs) and 500 dpi for line/tone combinations. Elsevier
accepts the following file formats for author artwork: TIFF, EPS, MS Word, PowerPoint and Excel. Additional details are available from
http://www.elsevier.com/artworkinstructions.
(g) Image processing. All digitized images must be of high quality
and have resolutions of at least 300dpi. Images should be minimally processed (for instance, to add arrows to a micrograph or delete
extraneous areas from a gel). It is essential that the final image correctly and accurately represents the original data. The Editors
reserve the right to request that the original unprocessed data be supplied as part of their evaluation of submitted manuscripts.
11. Cover Suggestions for cover illustrations should accompany accepted manuscripts. Cover illustrations may be
either in color or in black and white, and the illustration need not correspond to a figure in the paper. Cover illustrations should
illustrate a key point raised by the paper and be immediately recognizable. For structural studies this can be an aspect of the structure,
but stereo diagrams should be avoided. For biological studies a diagram illustrating a mechanism is often effective, but other types
of illustrations, including gels and other types of experimental data, can be used in the context of the cover.
The cover illustration
will appear in a landscape format, 103 mm 162 mm. A short descriptive legend should be supplied along with the figure. The legend should
be no longer than one sentence and supply information about the general topic rather than detailed information about the figure.
12. Alterations made in proof
One set of page proofs in PDF format will be sent by e-mail to the corresponding author, to
be checked for typesetting/editing. Proofreading is the author's responsibility.
Manuscripts are technically edited to comply with
the Journal style. Authors may therefore observe some changes whose intention is to ensure consistent representation and style for JMB
articles. Whilst you may request proof corrections, these may not be made if they contradict these style guidelines.
The Publisher
reserves the right to charge authors the cost of changes made to the text or figures at the proof stage when such changes are extensive.
Elsevier will do everything possible to get your article corrected and published as quickly and accurately as possible. In order to
do this we need your help. When you receive the (PDF) proof of your article for correction, it is important to ensure that all of your
corrections are sent back to us in one communication. Subsequent corrections will not be possible, so please ensure your first sending
is complete. Note that this does not mean you have any less time to make your corrections, just that only one set of corrections will
be accepted.
13. Copyright/offprints
Authors submitting a manuscript do so on the understanding that if it is accepted
for publication, exclusive copyright of the paper shall be assigned to the Publisher. Upon acceptance of an article authors will be asked
to transfer copyright (for more information on copyright see http://www.elsevier.com/copyright).
This transfer will
ensure the widest possible dissemination of information. A letter will be sent to the corresponding author confirming receipt of the
manuscript. A form facilitating transfer of copyright will be provided. If excerpts from other copyrighted works are included, the author(s)
must obtain written permission from the copyright owners and credit the source(s) in the article.
Elsevier has preprinted forms for
use by authors in these cases: contact ES Global Rights Department, P.O. Box 800, Oxford, OX5 1DX, UK; phone: (+44) 1865 843830, fax:
(+44) 1865 853333, email: permission@elsevier.com. The Publisher will not put any limitation on the personal freedom of
the author to use material contained in the paper in other works. In consideration for the assignment of copyright, the corresponding
author, at no cost, will be provided with 25 free paper offprints or, alternatively, a PDF file of the article via e-mail.
The PDF
file is a watermarked version of the published article and includes a cover sheet with the journal cover image and a disclaimer outlining
the terms and conditions of use. Further offprints may be ordered at extra cost at the proof stage. Correspondence regarding offprints
should be directed to: Global Author Support, Elsevier Science Ireland Ltd, Elsevier House, Brookvale Plaza, East Park, Shannon, Co.
Clare, Ireland; e-mail: epsupport@elsevier.com
14. Supplementary material
The acceptance of supplementary
material is at the Editor's discretion. Reference to its availability will be made in the printed paper. Please strictly follow the guidelines
below to ensure that this material is usable:
(a) Manuscripts must not refer to supplementary material throughout the
text.
(b) Supplementary material must be submitted electronically in final form and must be supplied as a separate file
from the text and figures.
ACCEPTABLE DATA
Full details are available from http://www.elsevier.com/artworkinstructions.
Please refer to the section on Multimedia files. Please note that permission to reproduce material previously made available electronically
is required in the same way that permission is necessary to reproduce illustrations or other material from previously published sources.
15. Representation of figures
Each individual figure or graphic must be supplied as a separate, stand-alone
file.
Artwork should not be embedded within the manuscript. It must be supplied in an electronic file separate
from the file that contains the manuscript. TIFF, EPS, PPT, and high-resolution PDF files are acceptable for artwork.
Figure and table files must be named with their respective numbers and graphic type such as Fig1.tif, Fig2a.tif, Table1. eps, etc. Long
file names are not acceptable.
When creating figures, use font sizes and line weights that will reproduce clearly and accurately
when figures are sized to the appropriate column width.
Do not include figure legends in a graphic file. Figure legends
should be placed after the Reference section as text in the main manuscript file.
Effort should be made to save figures
to formats most compatible to the program used to create them. For example, figures created in vector-based programs like Illustrator
(commonly used for graphs and line drawings) should be saved as PowerPoint files to maintain clean lines. Figures prepared in raster-based
programs like Photoshop can be
saved as TIFF. If it is necessary to export graphics from vector-based drawing programs (e.g., Illustrator)
to raster-based programs (e.g., Photoshop), a resolution of at least 1200 dpi is required for quality reproduction.
When
art is scanned for publication, a resolution of 1000 dpi is required for line art, 300 dpi for halftones (photographs) and 500 dpi for
line/tone combinations.
A consistent font style and size should be used in all figures.
16. Permissions
Authors seeking permission to reproduce Tables or Figures from articles published in JMB should send details of the material
they wish to reproduce to:
Elsevier Global Rights Department
P.O. Box 800
Oxford OX5 1DX, UK Tel: (+44) 1865 843830
Fax: (+44) 1865 853333 E-mail: permissions@elsevier.com
You may also contact Global Rights directly through Elsevier's
home-page (http://www.elsevier.com) by selecting 'Obtaining Permissions'.
NOTE: Authors do not need to obtain permission
to reproduce a figure that they have previously published in JMB if it is for a paper that is to be submitted to JMB.
HOW TO SUBMIT TOJMB
NEW SUBMISSIONS
At the time of submission, authors will be asked to choose one
of the following subject areas to which their manuscript is best suited: Gene structure and regulation Molecular genetics
of prokaryotes and eukaryotes DNA replication, recombination and repair RNA synthesis, metabolism and catalysis Molecular
basis of developmental biology Cell biology, signal transduction and motility Synthesis, trafficking and sorting of macromolecules
Virus and bacteriophage genetics and growth cycle
Manuscripts submitted in one of these subject areas will be allocated automatically
to Dr Jonathan Karn. All correspondence should be sent to jmb@elsevier.com
Dr Jonathan Karn, Executive Editor
c/o Journal of Molecular Biology 525 B Street, Suite 1900 San Diego, CA 92101-4495, USA Tel: +1 619 699 6234 Fax: +1
619 699 6859 E-mail: jmb@elsevier.com
Membrane structure and transport
Protein and nucleic acid structure,
function and interactions
Protein and RNA folding
Structure of viruses and supramolecular assemblies
Computational molecular
biology and bioinformatics
Manuscripts submitted in one of these subject areas will be allocated automatically to Dr Peter Wright.
All correspondence should be sent to jmb@scripps.edu
Dr Peter Wright, Editor-in-Chief Department of Molecular
Biology The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037, USA Tel: +1 858 784 9797
Fax: +1 858 784 9851 E-mail: jmb@scripps.edu
It is a condition of publication that all manuscripts are written
in clear and grammatical English and be submitted to the Journal of Molecular Biology web site at http://ees.elsevier.com/jmb.
If you are unable to provide an electronic version of your paper, please contact the Editorial Office prior to submission (e-mail: jmb@elsevier.com;
telephone; 1 (619) 699-6342; fax: (619) 699-6859).
A PDF comprising all text and figures is acceptable for initial submission. When
submitting a revised manuscript, separate electronic files are required.
Each manuscript is to be accompanied by an electronic cover
letter outlining the basic findings of the paper and their significance. PDFs of all related manuscripts under consideration for publication
must also be included with the submitted manuscript.
Authors should suggest at least six competent reviewers in their field and
may also suggest individuals whom they wish to have excluded from the review process. The list should be included in the cover letter.
The corresponding author will receive a decision letter from the Editor. Revised manuscripts and correspondence concerning such manuscripts
should be addressed to the Editor at the address indicated on the decision letter.
Many acceptable papers require minor revision or
condensation. It is in the mutual interest of both the authors and the journal that amended manuscripts be returned promptly. A revised
paper will retain its original date of receipt only if it is received by the Editor within 60 days of the date of return to the author.
Acceptable file types. Most word-processing packages are acceptable; however, we prefer that authors use a recent version of
Microsoft Word or Corel WordPerfect. Manuscripts saved with formatting intact are preferred. Rich-text format (.rtf extension) is acceptable,
but plain text (.txt extension) files are discouraged. Submit each figure as a separate TIFF or EPS file.
Once a paper is accepted,
JMB cannot use PDF or PostScript files because they do not allow editing of the text. Files created in layout programs such as Adobe
FrameMaker or PageMaker, QuarkXPress, and Corel Ventura are unacceptable. Artwork should not be embedded within the manuscript. It must
be supplied in electronic files separate from the manuscript file.
The submission of a manuscript is taken to imply that the material
is original, and that no similar paper has been or will be submitted for publication elsewhere. Submission of a manuscript will also
be taken to imply that all the named authors have seen and agreed to the submitted version of the paper, that all those listed as providers
of personal communications have agreed to their inclusion and that all requisite permissions for the use of material from previously
published sources or made available electronically, are supplied with the final submission.
Manuscripts and figures will not automatically
be returned to authors.
Manuscripts are technically edited to comply with the Journal style. You may therefore observe some changes
whose intention is to ensure consistent representation and style for JMB articles. Whilst you may request proof corrections, these may
not be made if they contradict these style guidelines.
REVISED / ACCEPTED PAPERS SUBMISSION CHECKLIST
Include
separate electronic source files for text, each figure, and each table.
Ensure that figure files are provided in an acceptable
file type, as close to the original source file as possible. Acceptable file types include TIF, EPS, PPT, PDF, and high-resolution JPG
files.
Ensure that manuscript text files are in an editable format such as a document (.doc) or rich-text (.rtf) format.
Adobe (.pdf) and straight text (.txt) files are not acceptable.
Check to make sure that the following are included in the
manuscript text portion of your submission: running title, author(s), affiliation(s) including e-mail addresses, abstract, keywords,
text elements, references, figure legends, and footnotes.
Check to make sure that all symbols are properly displayed in
the manuscript text, including subscripts, superscripts, mathematical symbols, and foreign characters. Use your word-processing symbol
features, adjusting the font as necessary to ensure that each symbol appears correctly.
Remove any automated formatting
within the manuscript text that may not convert properly when typeset, such as automated numbering or bulleting, automated footnotes,
and linked references.
