期刊名称：JOURNAL OF MOLECULAR GRAPHICS & MODELLING
 期刊简介(About the journal)
投稿须知(Instructions to Authors)
编辑部信息(Editorial Board)
About the journal
The JOURNAL OF MOLECULAR GRAPHICS AND MODELLING is a bimonthly update of the latest international developments in computer-aided molecular design. Through fully refereed research papers, short communications, reports from relevant conferences, book reviews, news, and a calendar of events, each issue offers detailed appraisals of current techniques along with full-color plates illustrating the exciting images these techniques can produce.
The journal's scope includes hardware and software, algorithms and procedures, representation of molecular structure, parametric plots, molecular modeling, and project results.
Instructions to Authors
Published in Affiliation with the Molecular Graphics and Modelling Society and the ACS Division of Computers in Chemistry
Former title: Journal of Molecular Graphics
Guide for Authors
Scope: The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in experimental and 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.
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 be 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.
Submissions: Send four (4) copies of the complete manuscript including illustrations to either Editor:
Professor Jonathan W. Essex, Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
Professor Andrew J. Holder, Department of Chemistry, Robert H. Flarsheim Hall, Room 410H, University of Missouri-Kansas City, Kansas City, MO 64110, U.S.A. Dr Holder can be contacted via e-mail at holdera@umkc.edu, Tel: +1 816 235 2293, and Fax: +1 816 235 6543.
When submitting a manuscript, the corresponding author must supply an e-mail address in the cover letter. Most of the refereeing process is handled by e-mail. Moreover, proofs are sent as PDF files attached to an e-mail message.
Articles can be submitted via e-mail, however there can be problems with some mail systems if the file is very large. It is therefore important to precede an electronic submission with an email to the appropriate editor. If the manuscript, including figures, is too large for e-mail submission, then the file may be submitted on CD along with a hard copy version.
For electronic submissions, the following conditions must be met:
The article is prepared on a PC or an Apple Macintosh computer with Microsoft Word. Figures are directly embedded in the Word document. Thus only a single file has to be transmitted.
Equations are typed in Word, not by an Equation Editor because equations from the latter do not always interchange well between different platforms. Likewise special characters such as e with a grave accent or u with an umlaut do not always transmit well. The artwork, even if it contains color, must be understandable when viewed in black and white.
Files should be checked for computer viruses before being sent. Infected files will not be processed.
With either hard copy or electronic submission, several possible referees can be recommended in the cover letter (or e-mail). If you have had your preprint read by colleagues who can critique the significance of the work, include their names, addresses, and e-mail addresses in your cover letter.
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, published as expeditiously as possible. Acceptance will depend on the paper's significance, relevance, and quality of writing. Papers describing software development should comment on the availability of the software (see also notes on Program Section below). Only previously unpublished work will be considered and the submission of a technical article will imply 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.
There are no page charges. Color figures are published free of charge 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 ChemWeb http://www.chemweb.com . Also, ScienceDirect http://www.sciencedirect.com provides subscribing institutions with Internet access to remotely-stored full-text of journal files.
The editors also welcome authoritative review articles or commentaries on any aspect of molecular modelling and computational chemistry. If you are interested in contributing such material, you should first contact one of the Editors.
Manuscripts: The manuscript should be typed on only one side of the paper, double spaced (not space-and-a-half) throughout, including the tables, references, and figure captions. 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, including Chemical Abstracts, Medline, etc. (see http://elsevier.com/locate/jmgm/ for a complete list).
The preferred platform for preparing a manuscript is a word processor such as MS Word or WordPerfect running on a PC (under some version of Windows) or running on a Macintosh (under Mac OS). Left-justify the text, do not embed any page-layout instructions and 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 the Helvetica font for labels and text.
Manuscripts describing new structure determinations: Authors must submit the structural data to the Protein Data Bank http://www.rcsb.org or other recognized database. These data include atomic coordinates and either X-ray amplitudes and phases or nuclear magnetic resonance constraints and assignments. If the paper discusses a protein structure only at the level of the main-chain alpha carbon atoms, only these coordinates need to be deposited. Manuscripts will not be published until confirmation has been received from the author that the required information has been received by the database. In the absence of a specified release date, it will be assumed that the crystallographic information is available coincident with appearance of the publication.
Programs Section: The journal includes an occasional section where descriptions of new, publicly available computer programs can be published and is intended for programs that contain only small advances in new methods of visualisation or analysis, but provide an implementation of a set of tools that other scientists in the community will find useful. In general, the description of the program will occupy at most two sides of one page in the published journal, including one or two images which capture the important features of the program. We require that the programs are available free of charge and that reviewers test that the programs function in the manner described. The version of the program described in the article will be deposited on a web site maintained by the Molecular Graphics and Modelling Society. This web site listing can hold a more detailed description of the program, as well as links to the author's web pages for updated versions.
This Programs Section does not reduce the Journal's commitment to publish full articles describing new methods for data visualisation or analysis. A full article, however should include a detailed description of how the visualisation or analysis is performed (the methods and algorithms) and make comparison to existing methods, demonstrating the additional scientific insights that can be gained. This type of article could include a reference to a web site but the program does not necessarily have to be freely available.
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.
Indicate superscripts and subscripts clearly.
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 a table can be placed in footnotes to the table. Avoid the use of vertical rules, but horizontal rules can be used. Tables should not duplicate results presented in graphs.
Illustrations: 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 original camera-ready artwork for all illustrations (line, halftone, and color). Photocopies are not acceptable. For line art and halftones, submit original artwork from a high resolution laser printer. For color figures, submit high resolution prints or glossy photographs. All 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." 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 sheet of manuscript paper, clearly labeled, and not attached to the artwork. Upon request, original art will be returned to the author after publication.
Color illustrations: Color art is published within the body of an article without cost to the authors where deemed appropriate and required for clear communication 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 look closely at every color figure to ensure that it is necessary.
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. D.C. Spellmeyer, A.K. Wong, M.J. Bower, 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., C.H. Reynolds, Free energy perturbation study of octanol/water partition coefficients: Comparison with continuum GB/SA calculations. J. Phys. Chem. B 103 (1999) 714-726.
3. J. Gao, Methods and applications of combined quantum mechanical and molecular mechanical potentials. In: K.B. Lipkowitz, and D.B. Boyd (Eds.), Reviews in computational chemistry, VCH Publishers, New York, 7(1995) 119-185.
4. M.P. Allen, D.J. Tildesley, Computer simulation of liquids. Clarendon, Oxford, 1987.
5. Spartan, version 4.1.1, 1993, Wavefunction, Inc., Irvine, Calif.
Computer Disks: Send either hard copy or e-mail when first submitting your paper for review. After your paper has been refereed and revised if necessary, the final version should be submitted in both hard copy and disk forms. Use a 3.5 inch HD diskette, a ZIP cartridge or a CD for the electronic documents. Make certain that the disk and hard copy match exactly. Label the diskette, CD or cartridge with your name and the title of the article. Make sure there are no computer viruses present; infected items will not be processed. Specify what software was used, including which release, e.g., MS Word 98, and what operating system version was used; either Windows XX (on a PC) or Macintosh OS (on an Apple) are acceptable. The electronic documents should include all textual material (text, references, tables, figure captions, etc.) and separate illustration files, if available. All artwork and tables should be also submitted in camera-ready hard copy.
Keep a back-up disk for reference and safety. If you have any questions about manuscript preparation, please contact the Editors.
If a revised manuscript is submitted more than six months after it was initially submitted, it will be considered a new submission.
For Final, Accepted Manuscripts
Once your article has been accepted, submit three paper copies of the final manuscript and a disk to the editor who is handling your manuscript. It is important that the file on disk and the printout(s) are identical. In order to create digital artwork for the final copy, please consult the Elsevier Science Electronic Artwork web site; http://www.elsevier.com/locate/authorartwork which contains appropriate instructions. Please note that Elsevier does not allow the submission of PowerPoint or other screen-produced digital files because they have poor resolution. Owing to reprographic quality requirements, also submit one clearly separated and labeled set of laser-printed, paper-copy figures.
Submit the final manuscript to the editor who is handling your article. Label diskettes with authors' names, manuscript number, computer operating system, and name of word processor. Ensure that the submitted electronic files exactly match paper copies.
Proofs: One set of proofs is sent as a PDF file attached to an e-mail message 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. The corrected proofs should be returned within 48 hours by air express.
Copyright: Before publication, authors are requested to assign copyright to Elsevier Science Inc. This allows the company to sanction reprints and photocopies and to authorize the reprinting of complete issues or volumes according to demand. Authors' traditional rights will not be jeopardized by assigning copyright in this manner, as they will retain the right to reuse their material and to veto third-party publications.
Reprints: The corresponding author of an article published in the journal is entitled to receive 25 free reprints. Additional reprints may be ordered using the reprint order form sent to the author with proofs.
Editorial Board
- Editor:
- Dr J.W. Essex, Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK Tel: +44 (0) 23-8059-2794, Fax: +44 (0) 23-8059-3781, Email: j.w.essex@soton.ac.uk
- US Editor:
- A.J. Holder, Department of Chemistry, Robert H. Flarsheim Hall, Room 410H, University of Missouri-Kansas City, Kansas City, MO 64110 U.S.A. Tel: +1.816.235 2293, Fax: +1. 816. 235 6543, Email: holdera@umkc.edu
- International Editorial Board:
- Dr. D.K. Agrafiotis, 3-Dimensional Pharmaceuticals, Exton, Pennsylvania, USA
Prof. J. Aqvist, Uppsala University, Uppsala, Sweden
Dr. F.E. Blaney, Glaxo Smith Kline, Harlow, Essex, UK
Dr. H.-J. Boehm, Hoffman-la-Roche, Basel, Switzerland
Dr. R.G.A. Bone, Pennie & Edmonds, LLP, 3300 Hillview Avenue, Palo Alto, CA 94304, USA
Prof. J.P. Bowen, University of Georgia, USA
D.B. Boyd, Indianapolis, USA
Prof. C.M. Breneman, Rensselaer Polytechnic Institute, Troy, New York, USA
Dr. H. Broughton, Lilly S.A., Madrid, Spain
Dr. A. Caflisch, University of Zurich, Zurich, Switzerland
Prof. C. Cambillau, University of Marseille, Marseille, France
Dr. P.-A. Carrupt, Universite de Lausanne, Lausanne, Switzerland
Dr. G.R. Famini, USABCCOM/ECBC, Aberdeen Proving Ground, USA
Prof. M.M. Francl, Bryn Mawr College, Bryn Mawr, USA
Dr. A.C. Good, Bristol-Myers Squibb, Wallingford, Connecticut, USA
Dr. J.M. Goodman, University of Cambridge, Cambridge, UK
Prof. J.R. Grigera, Universidad Nacional de La Plata, La Plata, Argentina
R. Hubbard, York , UK Tel: (44)1904-432569, Fax: (44)1904-410519, Email: rod@yorvic.york.ac.uk
Dr. R. Lewis, Lilly Research Centre, Windlesham, Surrey, UK
Prof. T. Liljefors, Royal Danish School of Pharmacy, Copenhagen, Denmark
Dr. B. Maigret, Henri Poincare University, Nancy, France
Prof. G. Náray-Szab?/B>, Lorand Eötvös University, Budapest, Hungary
Dr. T.I. Oprea, University of New Mexico, Albuquerque, USA
Dr. C.H. Reynolds, Rohm and Haas Company, Spring House, Pennsylvania, USA
Dr. Mark Sansom, University of Oxford, Oxford, UK
Dr. R.P. Sheridan, Merck Research Laboratories, Rahway, New Jersey, USA
Prof. Z. Slanina, Academia Sinica, Nankang, Taipei, Taiwan ROC
Dr. D.C. Spellmeyer, Oakland, CA, USA
Dr. M.J.E. Sternberg, Imperial Cancer Research Fund, London, UK
Prof. A. Tropsha, University of North Carolina, Chapel Hill, North Carolina, USA
Dr. M. Vieth, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, Indiana, USA
Dr. R. Wade, European Media Laboratory, Heidelberg, Germany
Dr. M. Waldman, 9685 Scranton Rd, San Diego, CA 92121, USA
Dr W.J. Welsh, New Jersey, USA
Prof. E. Westhof, University of Strasbourg, Strasbourg, France
Prof. R.A. Wheeler, University of Oklahoma, Norman, Oklahoma, USA
Prof. P. Willett, University of Sheffield, Sheffield, UK
Dr. D.A. Winkler, Commonwealth Scientific and Industrial Research Organisation, Clayton South, Australia
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