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.
Submissions:
Submissions to JMGM are ONLY accepted through Elsevier's online
submission system at:
When submitting via the EES website, you will be guided stepwise
through the creation and uploading of the various files and data, among others a submission letter and the names and addresses (including
e-mail) of at least three possible referees. The last stage of submitting your manuscript is selecting one of our Editors (see information
below) you wish to handle your manuscript. Various formats are allowed for the initial submission, including PDF files. The final revision
must be as a Word or other suitable word processor document. When a Word or equivalent document is uploaded as the initial submission,
the system automatically generates an electronic (PDF) proof, which is then used for reviewing. All correspondence, including the editor's
request for revision and final decision, will be by e-mail.
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.
General: A copy of these instructions
to authors is available online at http://www.elsevier.com/locate/jmgm/ which also has pertinent information about the journal.
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.
Page charges and reprints
There are no
page charges. Colour illustrations will always be processed without charges for appearance on the electronic version of the journal.
In addition, they can be reproduced in print as well, if deemed appropriate by the Editors. Accepted papers will appear both in print and on the World Wide Web, with online access available to individuals through ScienceDirect http://www.sciencedirect.com/.
The corresponding author, at no cost, will be provided with a PDF file of the article via e-mail or, alternatively, 50 free paper offprints.
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 printed reprints can be ordered at prices shown on the reprint order form which
will be sent to the author on receipt of the accepted manuscript by the publisher.
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.
Revised manuscripts must be resubmitted within ninety days of return of reviewer
comments.
Copyright transfer
Upon acceptance of an article, authors will be asked to sign 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 (or letter) 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.
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Use wide margins of about 4 cm (1.5 inches). The font should be at least 12 point size. Number every sheet in one sequence starting from
the title page. Papers should be arranged in the following order: title; names of authors; address(es) of the place(s) at which the work
was carried out; an abstract of 150-250 words outlining the work and highlighting significant conclusions of the paper; keywords (at
least five); introduction, methodology, results, discussion, conclusions, acknowledgments (if any); references; tables (each on a separate
page); captions to figures (together on one or more pages); and figures (each on a separate page). The title and abstract should be carefully
worded to aid in retrieving the article from abstracting and database services.
Left-justify the text and do not embed any page-layout
instructions. Please disable automatic end-of-line hyphenation.
Trade names should be clearly identified. 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.
For chemical structure diagrams, use one of the standard chemical drawing software packages such as ChemDraw. Use Helvetica font for
labels and text.
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.
Tables: Number tables consecutively through the paper (with Arabic numerals) referring to them in the
text as Table 1, Table 2, etc., with a short caption at the top of each table. Longer explanations of contents on a table can be placed
in footnotes to the table. Avoid the use of vertical rules, but horizontal rules are allowed. Design tables to be self-explanatory, and
do not duplicate data in text or illustrations.
Illustrations and Figures: To create digital artwork, please consult the Elsevier
Electronic Artwork web site; http://www.elsevier.com/artworkinstructions, which contains appropriate instructions. Please
note that Elsevier does allow the submission of MS Office files (Word, Powerpoint, Excel), provided they meet certain conditions (see
information given on above mentioned website). It is preferred to save files in EPS or TIFF format. Number figures consecutively through
the paper (with Arabic numerals), referring to them in the text as Figure 1, Figure 2, etc., with a short caption being provided for
each figure as appropriate. Likewise number schemes or other chemical diagrams consecutively through the paper (with bold Arabic numerals),
referring to them in the text as Scheme 1, Scheme 2, etc., with a short caption provided for each scheme as appropriate. It is the author's
responsibility to provide high-quality electronic images of all figures, graphs, and/or illistrations). All such artwork should be in
high resolution; figure annotations or images with jagged edges are not suitable. Color drawings should be designed to have easily distinguishable
colors. Each piece of art should be carefully labeled with the author's name and figure number, i.e., "Jones et al., Figure 3." If artwork
is provided as separate files upon submission, name the files in a consistent manner as above. Indicate the top of the figure if not
obvious. In order to stand up well during reduction for publication, lines in artwork should be no less than 1 point width. Use Helvetica
font for labels and annotations in figures. Figure, table and scheme captions should be typed together on a separate, clearly labeled
page and not attached to the artwork.
Color illustrations: Color art is published within the body of an article without cost
to the authors where required for clear communication and deemed appropriate by the Editors. However, because of the high costs of such
printing, authors are requested to use black and white tone figures wherever possible. The Editors will examine each color figure to
ensure that it is necessary.
Supplementary Material: JMGM invites authors of articles submitted for publication to provide
supplementary material in electronic form. Supplementary material that does not appear in the print version of an article can be found
online on ScienceDirect (http://www.sciencedirect.com).
Supplementary material (even though not printed) is an integral
part of a journal article and therefore will be sent to the reviewers along with the manuscript. Because this material will be mounted
exactly as submitted by the author, we recommend that the material be presented in an electronic format that is readily accessible to
the community. To ensure that your submitted material is directly usable, please provide the data 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. For more detailed instructions please visit our artwork instruction pages at http://www.elsevier.com/artworkinstructions.
Please note, however, that supplementary material will not appear in the printed journal.
References: Number all references
in a single sequence in the order in which they are first mentioned in the text. Any references in the tables should be cited according
their number in the text. References, numbered using Arabic numbers, should take the following form. Include titles and inclusive pagination
of articles and book chapters. Include all coauthors of each reference; use of "et al." is acceptable in the body of a manuscript, but
not in the references. Use the following style for journal articles, book chapters, books, and software:
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.
Proofs: One set of galley proofs is sent to the corresponding author prior to publication. Authors are responsible for
ensuring that manuscripts (whether original or revised) are accurate, so that extensive changes to proofs will not be necessary. Extensive
changes in results or conclusions at the proofs stage will require editorial approval. Authors may be charged for excessive alterations
in proofs.
Elsevier now sends PDF proofs which can be annotated; for this you will need to download Adobe Reader version 7 available
free from http://www.adobe.com/products/acrobat/readstep2.html. Instructions on how to annotate PDF files will accompany
the proofs. If you do not wish to use the PDF annotations function, you may list the corrections (including replies to the Query Form)
and return 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. The proofs should be returned within 48 hours.
Funding
body agreements and policies
Elsevier has established agreements and developed policies to allow authors who publish in Elsevier
journals 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
