Guide for Authors
Former title: Journal of Molecular Graphics
Published in Affiliation with the
Molecular Graphics and Modelling Society and the ACS Division of Computers in Chemistry Former title:
Journal of Molecular Graphics
Scope
The
Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers
in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects
of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations,
protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining,
and compound library design.
As a primary research journal,
JMGM seeks to bring new knowledge to the attention of our readers.
As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented.
Authors are strongly encouraged to bear this in mind when preparing manuscripts.
JMGM is published in association with two
of the largest and most active professional societies in the field: the Molecular Graphics and Modelling Society (MGMS) and the Computers
in Chemistry (COMP) Division of the American Chemical Society. Several thousand computational chemists worldwide belong to these two
societies and any research topic that may of interest to the membership is within the wide scope of the journal. It is not necessary
to be a member of these professional societies to publish in the journal.
Programs
Descriptions of programs will not be
accepted for publication by JMGM, but descriptions of
algorithms are acceptable.
Supplementary Information
Authors
should carefully develop manuscripts with brevity and clarity in mind, and as much material as possible should be deposited online as
Supplementary Information. Consider placing items that are not REQUIRED for understanding the main conclusions of the paper, but are
necessary for the reasons of repeatability and more detailed analysis in this category.
Types of paper
The editors also welcome authoritative review articles or commentaries on any aspect of molecular modeling
and computational chemistry. If you are interested in contributing such material, you should first contact one of the Editors.
Page Charges
This journal has no page charges.
Ethics in Publishing
For information on Ethics in Publishing and Ethical
guidelines for journal publication see
http://www.elsevier.com/publishingethics and
http://www.elsevier.com/ethicalguidelines.
Conflict of interest
All authors are requested to disclose any actual or potential conflict of interest
including any financial, personal or other relationships with other people or organizations within three years of beginning the submitted
work that could inappropriately influence, or be perceived to influence, their work. See also
http://www.elsevier.com/conflictsofinterest.
Submission declaration
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 copyright-holder.
Copyright
Upon acceptance
of an article, authors will be asked to complete a 'Journal Publishing Agreement' (for more information on this and copyright see
http://www.elsevier.com/copyright).
Acceptance of the agreement will ensure the widest possible dissemination of information. An e-mail will be sent to the corresponding
author confirming receipt of the manuscript together with a 'Journal Publishing Agreement' form or a link to the online version of this
agreement.
Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation
within their institutions. Permission of the Publisher is required for resale or distribution outside the institution and for all other
derivative works, including compilations and translations (please consult
http://www.elsevier.com/permissions). 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: please consult
http://www.elsevier.com/permissions.
Retained author rights
As an author you (or your employer or institution) retain certain rights; for details
you are referred to:
http://www.elsevier.com/authorsrights.
Role of the
funding source
You are requested to identify who provided financial support for the conduct of the research and/or preparation
of the article and to briefly describe the role of the sponsor(s), if any, in study design; in the collection, analysis and interpretation
of data; in the writing of the report; and in the decision to submit the paper for publication. If the funding source(s) had no such
involvement then this should be stated. Please see
http://www.elsevier.com/funding.
Funding body agreements and policies
Elsevier has established agreements and developed policies to allow authors whose
articles appear in journals published by Elsevier, to comply with potential manuscript archiving requirements as specified as conditions
of their grant awards. To learn more about existing agreements and policies please visit
http://www.elsevier.com/fundingbodies.
Language and language services
Please write your text in good English (American or British usage is accepted,
but not a mixture of these). Authors who require information about language editing and copyediting services pre- and post-submission
please visit
http://www.elsevier.com/languagepolishing or our customer support site at
http://epsupport.elsevier.com
for more information. Please note Elsevier neither endorses nor takes responsibility for any products, goods or services offered by outside
vendors through our services or in any advertising. For more information please refer to our Terms & Conditions:
http://www.elsevier.com/termsandconditions.
Submission
Submission to this journal proceeds totally online and you will be guided stepwise through
the creation and uploading of your files. The system automatically converts source files to a single PDF file of the article, which is
used in the peer-review process. Please note that even though manuscript source files are converted to PDF files at submission for the
review process, these source files are needed for further processing after acceptance. All correspondence, including notification of
the Editor's decision and requests for revision, takes place by e-mail removing the need for a paper trail.
For submitting your manuscripts to the
Journal of Molecular Graphics and Modelling please go to our
Elsevier Editorial System (EES) Website at:
http://ees.elsevier.com/jmgm .
Referees
Due to the substantial increase in the number of papers submitted, we require authors to submit the names and
email addresses of at LEAST two qualified referees along with their MS. These proposed referees should NOT be generally affiliated with
the author. A key place to locate such knowledgeable reviewers is from authors of the key papers in your references or online searches
using the keywords that have been specified.
All articles, notes, reviews, and communications will be refereed promptly by experts
and, if accepted, be published as expeditiously as possible. Acceptance will depend on the paper's significance, relevance, and quality
of writing. Only previously unpublished work will be considered and the submission of a technical article will carry with it the guarantee
that the work has not been published elsewhere. The author(s) also agree that the paper, if accepted, will not be published elsewhere
in the same form, in any language, without the consent of the copyright holder. It is the author's responsibility to obtain written permission
to reproduce material that has appeared in another publication.
All contributions submitted will be refereed at the discretion of
the editors. The editors reserve the right to reject manuscripts and to edit contributions when necessary. Submitted manuscripts will
be evaluated for completeness, English language quality and bibliographic content and may be returned to the authors immediately for
deficiencies in any of these areas. The official publication language of the Journal is English, and as such all papers that are submitted
must have high standards of English grammar so that the scientific content can be coherently communicated to our readers.
Use of wordprocessing software
It
is important that the file be saved in the native format of the wordprocessor used. The text should be in single-column format. Keep
the layout of the text as simple as possible. Most formatting codes will be removed and replaced on processing the article. In particular,
do not use the wordprocessor's options to justify text or to hyphenate words. However, do use bold face, italics, subscripts, superscripts
etc. Do not embed "graphically designed" equations or tables, but prepare these using the wordprocessor's facility. When preparing tables,
if you are using a table grid, use only one grid for each individual table and not a grid for each row. If no grid is used, use tabs,
not spaces, to align columns. The electronic text should be prepared in a way very similar to that of conventional manuscripts (see also
the Guide to Publishing with Elsevier:
http://www.elsevier.com/guidepublication). Do not import the figures into the text
file but, instead, indicate their approximate locations directly in the electronic text and on the manuscript. See also the section on
Electronic illustrations.
To avoid unnecessary errors you are strongly advised to use the "spell-check" and "grammar-check" functions
of your wordprocessor.
LaTeX
If the LaTeX file is suitable, proofs will
be produced without rekeying the text. The article should preferably be written using Elsevier's document class "elsarticle", or alternatively
the standard document class "article".
The Elsevier LaTeX style file package (including detailed instructions for LaTeX preparation)
can be obtained from the Quickguide:
http://www.elsevier.com/latex. It consists of the file: elsarticle.cls, complete user
documentation for the class file, bibliographic style files in various styles, and template files for a quick start.
Essential title page information
•
Title.
Concise and informative. Titles are often
used in information-retrieval systems. Avoid abbreviations and formulae where possible.
•
Author names and affiliations.
Where the family name may be ambiguous (e.g., a double name), please indicate this clearly. Present the authors' affiliation addresses
(where the actual work was done) below the names. Indicate all affiliations with a lower-case superscript letter immediately after the
author's name and in front of the appropriate address. Provide the full postal address of each affiliation, including the country name,
and, if available, the e-mail address of each author.
•
Corresponding author.
Clearly indicate who will handle
correspondence at all stages of refereeing and publication, also post-publication.
Ensure that telephone and fax numbers (with country
and area code) are provided in addition to the e-mail address and the complete postal address.
•
Present/permanent
address.
If an author has moved since the work described in the article was done, or was visiting at the time, a "Present address"
(or "Permanent address") may be indicated as a footnote to that author's name. The address at which the author actually did the work
must be retained as the main, affiliation address. Superscript Arabic numerals are used for such footnotes.
Keywords
Immediately after the abstract provide a minimum of 5 keywords. These keywords will be used for
indexing purposes.
Nomenclature and Units
Use of Systeme Internationale
(SI) units is encouraged; provide a conversion factor in parentheses at the first mention of non-SI units. Biochemical nomenclature should
conform to that recommended by the IUPAC-IUB Commission, and enzymes should be referred to by their recommended names and numbers.
Mathematical and Technical Terms
Write mathematical, Greek and other symbols carefully using, for instance,
a Symbol font. Explain the meaning of all symbols and acronyms in the text where they first occur. Identify Greek letters at their first
mention by writing their names in English words in the margin. If you use several symbols, a list of definitions -- not necessarily for
publication -- will be useful to and ensure the accuracy of the production editors. Identify all vectors, tensors, and matrices in bold.
The journal is read by an international audience; therefore authors should attempt to make their work clear to diverse readers. Note
the following points:
• Use a zero before decimal quantities less than one, e.g., 0.376, not .376.
• Group numbers
consisting of more than three numerals in threes separated by spaces, rather than commas.
• Use fractional exponents instead
of root signs, e.g., (3x + 9y)**1/2, not the square root symbol. (Here ** indicates that 1/2 is an exponent).
• Specify whether
logarithms are to base 10 or base e.
• Write simple mathematical fractions in the text on one line, e.g., L(N - l)/L(l), not
as a stacked fraction. If the fraction is complicated with superscripts and subscripts, then present it in a manner consistent with maximum
clarity.
Artwork
Electronic
artwork
General points
• Make sure you use uniform lettering and sizing of your original artwork.
•
Save text in illustrations as "graphics" or enclose the font.
• Only use the following fonts in your illustrations: Arial, Courier,
Times, Symbol.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention
for your artwork files.
• Provide captions to illustrations separately.
• Produce images near to the desired size of
the printed version.
• Submit each figure as a separate file.
A detailed guide on electronic artwork is available on our
website:
http://www.elsevier.com/artworkinstructions
You are urged to visit this site; some excerpts from the
detailed information are given here.
Formats
Regardless of the application used, when your electronic artwork is
finalised, please "save as" or convert the images to one of the following formats (note the resolution requirements for line drawings,
halftones, and line/halftone combinations given below):
EPS: Vector drawings. Embed the font or save the text as "graphics".
TIFF:
color or grayscale photographs (halftones): always use a minimum of 300 dpi.
TIFF: Bitmapped line drawings: use a minimum of 1000
dpi.
TIFF: Combinations bitmapped line/half-tone (color or grayscale): a minimum of 500 dpi is required.
DOC, XLS or PPT: If
your electronic artwork is created in any of these Microsoft Office applications please supply "as is".
Please do not:
•
Supply embedded graphics in your wordprocessor (spreadsheet, presentation) document;
• Supply files that are optimised for screen
use (like GIF, BMP, PICT, WPG); the resolution is too low;
• Supply files that are too low in resolution;
• Submit
graphics that are disproportionately large for the content.
Color artwork
Please make sure that artwork files are in an acceptable format (TIFF, EPS or MS Office files) and with the correct resolution. If,
together with your accepted article, you submit usable color figures then Elsevier will ensure, at no additional charge, that these figures
will appear in color on the Web (e.g., ScienceDirect and other sites) in addition to color reproduction in print. For further information
on the preparation of electronic artwork, please see
http://www.elsevier.com/artworkinstructions.
Tables
Number tables consecutively in accordance with their appearance in the text. Place footnotes to tables
below the table body and indicate them with superscript lowercase letters. Avoid vertical rules. Be sparing in the use of tables and
ensure that the data presented in tables do not duplicate results described elsewhere in the article.
References
Citation in text
Please ensure that
every reference cited in the text is also present in the reference list (and vice versa). Any references cited in the abstract must be
given in full. Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the
text. If these references are included in the reference list they should follow the standard reference style of the journal and should
include a substitution of the publication date with either "Unpublished results" or "Personal communication" Citation of a reference
as "in press" implies that the item has been accepted for publication.
Reference Style
1. Spellmeyer, D.C., Wong, A.K., Bower, M.J., and Blaney, J.M. Conformational analysis using distance geometry methods. J. Mol.
Graphics Modell. 1997, 15, 18-36.
2. Best, S.A., Merz, K.M. Jr., and Reynolds, C.H. Free energy perturbation study of octanol/water
partition coefficients: Comparison with continuum GB/SA calculations. J. Phys. Chem. B 1999, 103, 714-726.
3. Gao, J. Methods and
applications of combined quantum mechanical and molecular mechanical potentials. In: Reviews in computational chemistry, Lipkowitz, K.B.,
and Boyd, D.B., Eds., VCH Publishers, New York, 1995, Vol. 7, pp. 119-185.
4. Allen, M.P., and Tildesley, D.J. Computer simulation
of liquids. Clarendon, Oxford, 1987.
5. Spartan, version 4.1.1, 1993, Wavefunction, Inc., Irvine, Calif.
Commercial products,
including computer programs, are to be mentioned in the text of the manuscript and not normally referenced. If required the reference
should list the first author et al. only.
Supplementary material
Elsevier
accepts electronic supplementary material to support and enhance your scientific research. Supplementary files offer the author additional
possibilities to publish supporting applications, movies, animation sequences, high-resolution images, background datasets, sound clips
and more. Supplementary files supplied will be published online alongside the electronic version of your article in Elsevier Web products,
including ScienceDirect:
http://www.sciencedirect.com. In order to ensure that your submitted material is directly usable,
please ensure that data are provided in one of our recommended file formats. Authors should submit the material in electronic format
together with the article and supply a concise and descriptive caption for each file. Video files: please supply 'stills' with your files:
you can choose any frame from the video or make a separate image. These will be used instead of standard icons and will personalize the
link to your supplementary information. For more detailed instructions please visit our artwork instruction pages at
http://www.elsevier.com/artworkinstructions.
Submission checklist
It is hoped that this list will be useful during the final checking of an article
prior to sending it to the journal's Editor for review. Please consult this Guide for Authors for further details of any item.
Ensure
that the following items are present:
One Author designated as corresponding Author:
• E-mail address
• Full
postal address
• Telephone and fax numbers
All necessary files have been uploaded
• Keywords
• All figure
captions
• All tables (including title, description, footnotes)
Further considerations
• Manuscript has been "spellchecked"
and "grammar-checked"
• References are in the correct format for this journal
• All references mentioned in the Reference
list are cited in the text, and vice versa
• Permission has been obtained for use of copyrighted material from other sources
(including the Web)
• Color figures are clearly marked as being intended for color reproduction on the Web (free of charge)
and in print or to be reproduced in color on the Web (free of charge) and in black-and-white in print
• If only color on the
Web is required, black and white versions of the figures are also supplied for printing purposes
For any further information please
visit our customer support site at
http://epsupport.elsevier.com.
Use of the Digital Object Identifier
The Digital Object Identifier (DOI)
may be used to cite and link to electronic documents. The DOI consists of a unique alpha-numeric character string which is assigned to
a document by the publisher upon the initial electronic publication. The assigned DOI never changes. Therefore, it is an ideal medium
for citing a document, particularly 'Articles in press' because they have not yet received their full bibliographic information. The
correct format for citing a DOI is shown as follows (example taken from a document in the journal
Physics Letters B):
doi:10.1016/j.physletb.2003.10.071
When you use the DOI to create URL hyperlinks to documents on the web, they are guaranteed never to change.
Proofs
One set of page proofs (as PDF files) will be sent by e-mail to the corresponding author (if we do
not have an e-mail address then paper proofs will be sent by post) or, a link will be provided in the e-mail so that authors can download
the files themselves. Elsevier now provides authors with PDF proofs which can be annotated; for this you will need to download Adobe
Reader version 7 (or higher) available free from
http://www.adobe.com/products/acrobat/readstep2.html. Instructions on how
to annotate PDF files will accompany the proofs (also given online). The exact system requirements are given at the Adobe site:
http://www.adobe.com/products/acrobat/acrrsystemreqs.html#70win.
If you do not wish to use the PDF annotations function, you may list the corrections (including replies to the Query Form) and
return them to Elsevier in an e-mail. Please list your corrections quoting line number. If, for any reason, this is not possible, then
mark the corrections and any other comments (including replies to the Query Form) on a printout of your proof and return by fax, or scan
the pages and e-mail, or by post. Please use this proof only for checking the typesetting, editing, completeness and correctness of the
text, tables and figures. Significant changes to the article as accepted for publication will only be considered at this stage with permission
from the Editor. We will do everything possible to get your article published quickly and accurately. Therefore, it is important to ensure
that all of your corrections are sent back to us in one communication: please check carefully before replying, as inclusion of any subsequent
corrections cannot be guaranteed. Proofreading is solely your responsibility. Note that Elsevier may proceed with the publication of
your article if no response is received.
Offprints
The corresponding author,
at no cost, will be provided with 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. Additional paper
offprints can be ordered by the authors. An order form with prices will be sent to the corresponding author.
For inquiries relating to the submission of articles (including electronic submission
where available) please visit this journal's homepage. You can track accepted articles at
http://www.elsevier.com/trackarticle
and set up e-mail alerts to inform you of when an article's status has changed. Also accessible from here is information on copyright,
frequently asked questions and more. Contact details for questions arising after acceptance of an article, especially those relating
to proofs, will be provided by the publisher.
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