Guide for Authors
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.
Descriptions of programs will not be accepted for publication by JMGM, but descriptions of algorithms are acceptable.
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 papersStructural Data
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.
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/pdbe/), 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 JSB, 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 JMGM. The primary criteria for publication of a structure in JMGM are that it provides novel structural insights or important new functional and biological insights that are likely to be of general interest. 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. Further information and an example of a Conflict of Interest form can be found at: http://elsevier6.custhelp.com/app/answers/detail/a_id/286/p/7923/.
Submission declaration and verificationChanges to authorship
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 or as an electronic preprint, see http://www.elsevier.com/postingpolicy), 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, including electronically without the written consent of the copyright-holder. To verify originality, your article may be checked by the originality detection service CrossCheck http://www.elsevier.com/editors/plagdetect.
This policy concerns the addition, deletion, or rearrangement of author names in the authorship of accepted manuscripts:
Before the accepted manuscript is published in an online issue: Requests to add or remove an author, or to rearrange the author names, must be sent to the Journal Manager from the corresponding author of the accepted manuscript and must include: (a) the reason the name should be added or removed, or the author names rearranged and (b) written confirmation (e-mail, fax, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed. Requests that are not sent by the corresponding author will be forwarded by the Journal Manager to the corresponding author, who must follow the procedure as described above. Note that: (1) Journal Managers will inform the Journal Editors of any such requests and (2) publication of the accepted manuscript in an online issue is suspended until authorship has been agreed.
After the accepted manuscript is published in an online issue: Any requests to add, delete, or rearrange author names in an article published in an online issue will follow the same policies as noted above and result in a corrigendum.
CopyrightRetained author rights
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.
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 sourceFunding body agreements and policies
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 article for publication. If the funding source(s) had no such involvement then this should be stated. Please see http://www.elsevier.com/funding.
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.
• Articles are freely available to both subscribers and the wider public with permitted reuse
• An Open Access publication fee is payable by authors or their research funder
• Articles are made available to subscribers as well as developing countries and patient groups through our access programs (http://www.elsevier.com/access)
• No Open Access publication fee
All articles published Open Access will be immediately and permanently free for everyone to read and download. Permitted reuse is defined by your choice of one of the following Creative Commons user licenses:To provide Open Access, this journal has a publication fee which needs to be met by the authors or their research funders for each article published Open Access.
Creative Commons Attribution (CC-BY): lets others distribute and copy the article, to create extracts, abstracts, and other revised versions, adaptations or derivative works of or from an article (such as a translation), to include in a collective work (such as an anthology), to text or data mine the article, even for commercial purposes, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, and do not modify the article in such a way as to damage the author's honor or reputation.
Creative Commons Attribution-NonCommercial-ShareAlike (CC-BY-NC-SA): for non-commercial purposes, lets others distribute and copy the article, to create extracts, abstracts and other revised versions, adaptations or derivative works of or from an article (such as a translation), to include in a collective work (such as an anthology), to text and data mine the article, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, do not modify the article in such a way as to damage the author's honor or reputation, and license their new adaptations or creations under identical terms (CC-BY-NC-SA).
Creative Commons Attribution-NonCommercial-NoDerivs (CC-BY-NC-ND): for non-commercial purposes, lets others distribute and copy the article, and to include in a collective work (such as an anthology), as long as they credit the author(s) and provided they do not alter or modify the article.
Your publication choice will have no effect on the peer review process or acceptance of submitted articles.
The publication fee for this journal is $2600, excluding taxes. Learn more about Elsevier's pricing policy: http://www.elsevier.com/openaccesspricing.
Language (usage and editing services)Submission
Please write your text in good English (American or British usage is accepted, but not a mixture of these). Authors who feel their English language manuscript may require editing to eliminate possible grammatical or spelling errors and to conform to correct scientific English may wish to use the English Language Editing service available from Elsevier's WebShop http://webshop.elsevier.com/languageediting/ or visit our customer support site http://support.elsevier.com for more information.
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 .
RefereesAll 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.
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 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 softwareLaTeX
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. 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). Note that source files of figures, tables and text graphics will be required whether or not you embed your figures in the text. See also the section on Electronic artwork.
To avoid unnecessary errors you are strongly advised to use the 'spell-check' and 'grammar-check' functions of your wordprocessor.
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 any of the other recognized classes and formats supported in Elsevier's electronic submissions system, for further information see http://www.elsevier.com/wps/find/authorsview.authors/latex-ees-supported.
The Elsevier 'elsarticle' 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. For information about reference management please go to the document at http://cdn.elsevier.com/assets/pdf_file/0011/109388/elsdoc.pdf and click on the section 'bibliography'.
Essential title page informationGraphical abstract
• 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 phone numbers (with country and area code) are provided in addition to the e-mail address and the complete postal address. Contact details must be kept up to date by the corresponding author.
• 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.
A Graphical abstract is mandatory for this journal. It should summarize the contents of the article in a concise, pictorial form designed to capture the attention of a wide readership online. Authors must provide images that clearly represent the work described in the article. Graphical abstracts should be submitted as a separate file in the online submission system. Image size: please provide an image with a minimum of 531 × 1328 pixels (h × w) or proportionally more. The image should be readable at a size of 5 × 13 cm using a regular screen resolution of 96 dpi. Preferred file types: TIFF, EPS, PDF or MS Office files. See http://www.elsevier.com/graphicalabstracts for examples.
Authors can make use of Elsevier's Illustration and Enhancement service to ensure the best presentation of their images also in accordance with all technical requirements: Illustration Service.
Highlights are mandatory for this journal. They consist of a short collection of bullet points that convey the core findings of the article and should be submitted in a separate file in the online submission system. Please use 'Highlights' in the file name and include 3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point). See http://www.elsevier.com/highlights for examples.
Immediately after the abstract provide a minimum of 5 keywords. These keywords will be used for indexing purposes.
Nomenclature and UnitsDatabase linking
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.
Elsevier encourages authors to connect articles with external databases, giving their readers one-click access to relevant databases that help to build a better understanding of the described research. Please refer to relevant database identifiers using the following format in your article: Database: xxxx (e.g., TAIR: AT1G01020; CCDC: 734053; PDB: 1XFN). See http://www.elsevier.com/databaselinking for more information and a full list of supported databases.
Mathematical and Technical Terms• Use a zero before decimal quantities less than one, e.g., 0.376, not .376.
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:
• 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. Electronic artwork
• Make sure you use uniform lettering and sizing of your original artwork.
• Embed the used fonts if the application provides that option.
• Aim to use the following fonts in your illustrations: Arial, Courier, Times New Roman, Symbol, or use fonts that look similar.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention for your artwork files.
• Provide captions to illustrations separately.
• Size the illustrations close to the desired dimensions of the printed version.
• Submit each illustration as a separate file.
A detailed guide on electronic artwork is available on our website:
You are urged to visit this site; some excerpts from the detailed information are given here.
If your electronic artwork is created in a Microsoft Office application (Word, PowerPoint, Excel) then please supply 'as is' in the native document format.
Regardless of the application used other than Microsoft Office, when your electronic artwork is finalized, 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 (or PDF): Vector drawings, embed all used fonts.
TIFF (or JPEG): Color or grayscale photographs (halftones), keep to a minimum of 300 dpi.
TIFF (or JPEG): Bitmapped (pure black & white pixels) line drawings, keep to a minimum of 1000 dpi.
TIFF (or JPEG): Combinations bitmapped line/half-tone (color or grayscale), keep to a minimum of 500 dpi.
Please do not:
• Supply files that are optimized for screen use (e.g., GIF, BMP, PICT, WPG); these typically have a low number of pixels and limited set of colors;
• Supply files that are too low in resolution;
• Submit graphics that are disproportionately large for the content.
Please make sure that artwork files are in an acceptable format (TIFF (or JPEG), EPS (or PDF)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.
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. 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 management softwareReference Style
This journal has standard templates available in key reference management packages EndNote (http://www.endnote.com/support/enstyles.asp) and Reference Manager (http://refman.com/support/rmstyles.asp). Using plug-ins to wordprocessing packages, authors only need to select the appropriate journal template when preparing their article and the list of references and citations to these will be formatted according to the journal style which is described below.
1. D.C. Spellmeyer, A.K. Wong, M.J.. Bower, and J.M. Blaney, Conformational analysis using distance geometry methods. J. Mol. Graphics Modell. 15 (1997) 18-36.
2. S.A. Best, K.M. Merz, Jr., and C.H. Reynolds, Free energy perturbation study of octanol/water partition coefficients: Comparison with continuum GB/SA calculations. J. Phys. Chem. B 103 (199) 714-726.3. J. Gao, Methods and applications of combined quantum mechanical and molecular mechanical potentials. In: Reviews in computational chemistry, K.B. Lipkowitz and D.B. Boyd, Eds., VCH Publishers, New York, 1995, Vol. 7, pp. 119-185.
4. M.P. Allen and D.J. Tildesley, 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.Video data
Elsevier accepts video material and animation sequences to support and enhance your scientific research. Authors who have video or animation files that they wish to submit with their article are strongly encouraged to include links to these within the body of the article. This can be done in the same way as a figure or table by referring to the video or animation content and noting in the body text where it should be placed. All submitted files should be properly labeled so that they directly relate to the video file's content. In order to ensure that your video or animation material is directly usable, please provide the files in one of our recommended file formats with a preferred maximum size of 50 MB. Video and animation files supplied will be published online in the electronic version of your article in Elsevier Web products, including ScienceDirect: http://www.sciencedirect.com. Please supply 'stills' with your files: you can choose any frame from the video or animation or make a separate image. These will be used instead of standard icons and will personalize the link to your video data. For more detailed instructions please visit our video instruction pages at http://www.elsevier.com/artworkinstructions. Note: since video and animation cannot be embedded in the print version of the journal, please provide text for both the electronic and the print version for the portions of the article that refer to this content.
Supplementary dataSubmission checklist
Elsevier accepts electronic supplementary material to support and enhance your scientific research. Supplementary files offer the author additional possibilities to publish supporting applications, high-resolution images, machine-readable files of datasets (especially compounds) 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 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.
The following list will be useful during the final checking of an article prior to sending it to the journal for review. Please consult this Guide for Authors for further details of any item.
Ensure that the following items are present:
One author has been designated as the corresponding author with contact details:
• E-mail address
• Full postal address
• Phone numbers
All necessary files have been uploaded, and contain:
• All figure captions
• All tables (including title, description, footnotes)
• Manuscript has been 'spell-checked' 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://support.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. Example of a correctly given DOI (in URL format; here an article in the journal Physics Letters B):
When you use a DOI to create links to documents on the web, the DOIs are guaranteed never to change.
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://get.adobe.com/reader. 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/reader/tech-specs.html.
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 – please let us have all your corrections within 48 hours. It is important to ensure that all 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 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). For an extra charge, paper offprints can be ordered via the offprint order form which is sent once the article is accepted for publication. Both corresponding and co-authors may order offprints at any time via Elsevier's WebShop (http://webshop.elsevier.com/myarticleservices/offprints). Authors requiring printed copies of multiple articles may use Elsevier WebShop's 'Create Your Own Book' service to collate multiple articles within a single cover (http://webshop.elsevier.com/myarticleservices/offprints/myarticlesservices/booklets).
For inquiries relating to the submission of articles (including electronic submission) please visit this journal's homepage. For detailed instructions on the preparation of electronic artwork, please visit http://www.elsevier.com/artworkinstructions. Contact details for questions arising after acceptance of an article, especially those relating to proofs, will be provided by the publisher. You can track accepted articles at http://www.elsevier.com/trackarticle. You can also check our Author FAQs at http://www.elsevier.com/authorFAQ and/or contact Customer Support via http://support.elsevier.com.