19th-banner-rev.gif

Instructions

Instructions to Authors

Subjects Covered, Policy and Philosophy

The Journal of Biomolecular Structure and Dynamics cordially welcomes manuscripts from active investigators in biological structure, dynamics, interactions and expression. Over the quarter of a century of its service to scientists, particularly in the last several years, it has evolved to be the mainstay of publications in high end computational science in atomic structural biology, bioinformatics, virtual drug design, genomics and biological networks- mainly an interdisciplinary computational journal in life sciences. It continues to augment the validity of theoretical studies by publishing appropriate papers in experimental sciences. The Journal publishes original articles, communications a la express and timely reviews. If an author wishes to write a review, please obtain clearance from any one of the editors.

While JBSD publishes high end research articles, we are also strongly devoted to using the journal to enhance doctoral education and to develop young scientists as outstanding structural biologists.These are times when many scientists find themselves with little time for discussion of academic research, and JBSD must double its effort to propagate core values of academic brilliance. Hence the manuscripts submitted to JBSD must be written so that it is accessible to nonspecialists and doctoral students.

Access data via Google Analytics indicate that JBSD is being visited on a continuing basis by some 7450 people each month from 100 countries. Below is a visitor graphic data for JBSD for India, China, UK, Germany, Japan, Brazil and Iran. If you are interested in the data for your country or your state within US, please email Editor-in-Chief Prof. Sarma.

india-china-visit.gif

uk-germany-japan.gif

iran-brazil.gif

Where the Manuscript Should be Sent?

A single msword.doc file of the complete manuscript (including text, tables and figures) should be submitted at the ScholarOne manuscript submission site:

http://mc.manuscriptcentral.com/jbsd

Supplementary materials of text, tables and figures can be uploaded as pdfs. Supplementray materials of movies can be uploaded in flash and other formats.


Board of Editors


Elena Bichenkova
Univ. of Manchester, UK
fone: 44 (0) 161 275 8359 fx: 44 (0)0161 275 2396
Elena.V.Bichenkova@manchester.ac.uk

Thomas E. Cheatham, III
University of Utah, USA
fone: 801 587 9652 fx: 801 585 5366
Email: tec3@utah.edu

Calvin Yu-Chian Chen
China Medical Univ., Taiwan
fone: 886-4-22053366-3326 fx: 886-4-22070465
ycc@mail.cmu.edu.tw

Miroslav Fojta
Academy of Science of the Czech Republic
fone: 420 541517197 fx: 420 541211293
fojta@ibp.cz

M. D. Frank-Kamenetskii
Boston University, USA
fone: 1 617 353 8498 fx: 1 617 353 8501
mfk@bu.edu

Yaakov (Koby) Levy
Weizmann Institute of Science, Israel
fone: 972-8-934-458; fx: 972-8-9344136
koby.levy@weizmann.ac.il

Vsevolod J. Makeev
Genetika, Moscow, Russia
fone: 7 495 315 0156 fx: 7 495 315 0501
vsevolod.makeev@gmail.com

Luis A. Marky
University of Nebraska Medical Center, USA
fone: 402 559-4628; fx: 402 559-9643
lmarky@unmc.edu

Aditya Mittal
Indian Institute of Technology Delhi, India
fone: 91 11 26591052; fx: 91 11 26582037
amittal@bioschool.iitd.ac.in

Dino Moras
IGBMC Parc d'Innovation, France
fone: 33-88-653351 fx: 33-88-653203
moras@igbmc.u-strasbg.fr

Anna Panchenko
NCBI, NLM, NIH, USA
fone: 1 301 435 5891 fx: 1 301 480 4637
panch@ncbi.nlm.nih.gov

Remo Rohs
Univ. of Southern California., USA
fone: 1 213-740-0552
rohs@usc.edu

Irina M. Russu
Wesleyan University, USA
fone: 860-685-2428 fx: 860-685-2141
irussu@wesleyan.edu

Wolfram Saenger
Freie University of Berlin, Germany
fone: 49 30 8383412; fx: 49 30 8386702
saenger@chemie.fu-berlin.DE

Ramaswamy H. Sarma, Editor-in-Chief
The University at Albany, SUNY, USA
fone: 1 518 456 9362: fx: 1 518 452 4955
rhs07@albany.edu

Zippora Shakked
Weizmann Institute of Science, Israel
fone: 972 8 482672 fx: 972 8 344154
zippi.shakked@weizmann.ac.il

R. Sowdhamini
National Center for Biological Sciences, India
fone: 91 80 23666002 fx: 91 80 23636662
mini@ncbs.res.in

J. Sponer
Academy of Sciences of the Czech Republic
fone: 420 5 4151 7133 fx: 20-5-4151-7133
sponer@ncbr.chemi.muni.cz

V. N. Uversky
University of South Florida
fone: 813 974 5816 fx: 813 974 7357
vuversky@health.usf.edu

Sybren S. Wijmenga
Radboud University Nijmegen
fone: 31 24 3652678; fx: 31 24 3652112
S.Wijmenga@nmr.ru.nl

Krystyna Zakrzewska
Institut de Biologie et Chimie des Proteines, France
fone: 33 4 37 65 29 44 fx: 33 4 72 72 26 04
krystyna.zakrzewska@ibcp.fr

Dmitry O. Zharkov
SB RAS Institute of Chemical Biology, Russia
fone: 7 383 363 5128 fx:: 7 383 363 5153
dzharkov@niboch.nsc.ru

Review by Referees

All articles will be subject to review by expert referees to ascertain scientific soundness. The purpose of the review is also to develop discussion and debate to evolve a consensus rather than to push anyone's personal agenda. Authors should suggest a slate of five possible referees. The editors may or may not employ the recommended referees.

Revised Versions

A complete msword.doc file including text, tables and figures; a pdf version of the .doc file, any supplementary matarials after revision all should be uploaded at the ScholarOne site indicated above.

Category of Articles

Regular Articles: No page limitations. Normal time for publication of papers which do not undergo extensive revisions is between 3 to 5 months.

Express Communications: Timely discoveries need to be communicated at an accelerated pace, that is, within 2 to 3 months. Authors wishing to have their manuscripts published express should indicate so in the covering letter along with the arguments for immediate communication. Express articles normally should not exceed 12 pages including tables and figures. Editors and referees may disagree with the author's request for express handling, and in this case the article will be processed for normal publication.

Hypotheses: Publication as immediately as possible. Not to exceed four printed pages, papers in this section must propose interesting models and ideas satisfying the following criteria:

  • New explanations, hypotheses of certain phenomenon, either recently observed facts not accounted for or well known facts whose "text book" explanations contradict new findings.
  • The new hypothesis cannot be easily proven at present.
  • There are specific ways to test the new hypothesis in the future, and short descriptions of these ways have to be presented.

Opinions: Publication as immediately as possible. Not to exceed 4 journal pages, papers in this section present new vision/perspective of recent developments; they may also critically address recent publications in any journal. In the latter case the criticized authors will be given a chance to write a prompt response. Articles in this section should primarily address unsolved controversies arising in current research.

Fonts, Special Characters, Spacing

For text, tables and figure legends, please use the font "Times;" for Greek letters and symbols, use the "Symbol" font or use appropriate key board equivalents under "Times."please embed fonts in the pdf. Font size should be 12 pts or higher, and the manuscript should be in double space. Make sure that the referees can read through the manuscript with out strain. Do not set in type the manuscript the way it looks when published.

Manuscript Organization

The manuscript may be arranged in the following manner: Introduction; Materials and Methods, Results and Discussion, Acknowledgments, and References. The Materials and Method section should give sufficient details so that the experiments can be repeated. The subheading "Results and Discussion" in many instances can be replaced by a set of appropriate subheadings which reflect the contents. In the Abstract section, if there is a reference, please provide the complete reference (rather than as bibligraphic citation). This is because PubMed, Chemical Abstracts and Biological Abstracts use the abstracts from the Journal directly.

The authors may place tables and figures close to where they should appear or present them together at the end. The legends for figures and tables should appear under the appropriate figure and on top of the tables, respectively. Figure and Table numbers must be marked clearly. They are numbered using the Arabic system (i.e. 1, 2, 3 ...).

Title Page

Do not use all CAPITAL LETTERS for any entry in the title page; use both lower and upper cases. The title page must contain:

  1. Title in upper and lower case
  2. Authors and their affiliation. In the case of authors who originate from different institutions, please include a complete mailing address for each institution.
  3. The author to whom correspondence should be addressed must be indicated by an asterisk along with his/her phone, fax and email data. This will appear as a footnote to page 1 of the article.
  4. A short title should appear on this page to be used as a running head.

References

Since Taylor and Francis took over the publication of JBSD, references within the text are cited by author's name and the year of publication and they appear in the Reference list alphabetically along with title of articles. Order the references in the Reference list alphabetically in the order of the author names. Names of journals and volume numbers appear in regular italic.

For a detailed presetation of the organization of various references please consult:

http://www.tandf.co.uk/journals/authors/style/reference/tf_A.pdf

Below is a quick, but incomplete, example of reference organization:

For half a century, prototropic tautomerism of nucleotide bases has been considered the origin of spontaneous point mutations arising in DNA ( Fu, Wang, Mab, & Zhang, 2011). Watson and Crick were the first to propose the classical hypothesis on the role of the so-called mutagenic tautomers in the origin of DNA point mutations. Later the tautomeric assumption was confirmed experimentally (Bebenek, Pedersen, & Kunkel, 2011; Harris et al., 2003; Sinha & Haimes, 1981) and grounded theoretically by means of modernquantum-chemical methods (Gorb et al., 2002).

Bebenek, K., Pedersen, L.C., & Kunkel, T.A. (2011). Replication infidelity via a mismatch with Watson-Crick geometry. Proceedings of the National Academy of Sciences USA, 108, 1862–1867.

Fu, L.-Y., Wang, G.-Z., Mab, B.-G., & Zhang, H.-Y. (2011). Exploring the common molecular basis for the universal DNA mutation bias: revival of Löwdin mutation model. Biochemical and Biophysical Research Communications, 498, 367–371.

Gorb, L., Podolyan, Y., Leszczynski, J., Siebrand, W., Fernández-Ramos, A., & Smedarchina, Z. (2002). A quantum-dynamics study of the prototropic tautomerism of guanine and its contribution to spontaneous point mutations in Escherichia coli. Biopolymers, 61, 77–83.

Harris, V.H., Smith, C.L., Cummins, W.J., Hamilton, A.L., Adams, H., Dickman, M., … Williams, D.M. (2003). The effect of tautomeric constant on the specificity of nucleotide incorporation during DNA replication: support for the rare tautomer hypothesis of substitution mutagenesis. Journal of Molecular Biology, 326, 1389–1401.

Sinha, N.K., & Haimes, M.D. (1981). Molecular mechanisms of substitution mutagenesis. An experimental test of the Watson-Crick and topal-fresco models of base mispairings.Journal of Biological Chemistry, 256, 10671–10683.

If you are using Endnotes to cite your references and create the bibliography, download the Endnote plugin below specially created to generate citation and bibliography a la Taylor and Francis JBSD.

endnote-plugin-rev2.zip

After downloading, unzip the folder, and drag the plugin inside the folder into your style folder for Endnotes.

Footnotes


For page 1 to identify author affiliation, footnotes a, b, c .... appear as superscripts. All subsequent footnotes appear as superscripts, and the footnotes must be explained on the bottom of the page where they first appeared.

Supplementary Material


If your article contains supplementary material, please submit a PDF version of it as a separate file when the manuscript is submitted. Also, upload the supplementary material to your server and obtain the URL so that readers can download it from author's web site, free of charge. In addition, start a new paragraph, similar to the one below, under the title "Supplementary Material" and insert the paragraph just after the abstract.

Supplementray material dealing with ----------------- is available from the authors directly and can be downloaded free of charge from the author's server at the URL --------------.

Abbreviations


List them immeditely following the abstract; Authors must adhere to SI units; units are not italicized.

Equations

Mathematical equations should be clearly created and numbered in the text. The number should appear in square brackets, i.e., [ ]. Equations can be created using Words equation editor.Word 2007 for windows equations are not supported in word 2008 Mac. The Editor in Chief Prof. sarma uses a Mac and he cannot see your equations if you use Word 2007 for windows equations.

Nomenclature

The Journal follows IUPAC-IUB nomenclature.

No Page Charges

There are no page charges. Once a manuscript has been accepted by an Editor as scientifically sound, the Journal of Biomolecular Structure and Dynamics will publish the article at its expense.

No Color Charges

The use of color in articles dealing with biological structure and dynamics has become so routine that this journal publishes free of charge all color illustration at the PDF and HTML full text ONLINE versions. The printed book version is black and white by default, that is, figures that appear in color in the Online versions will appear black and white in the printed book version. However, the authors have the option of their figures appear in color in the printed book version, if they pay £250 (close to US $400) per figure. For more than 4 figures, each subsequent figure will be charged at £50/figure. To make this payment authors must contact Taylor and Francis when they receive the proofs. In view of the fact that very few people use the printed book version, color figures are optional for the authors.

Page Proofs

The authors will be furnished with PDF files. It is the author's responsibility that the proofs are corrected and returned immediately. If the proofs are not received on time Adenine will proof read and go ahead with the production. Author's reasonable number of corrections will be incorporated at no charge. All other alterations and corrections will be charged to the author. Authors are completely responsible for obtaining the permission to reproduce materials such as figures, copyrighted text etc by a publisher/agency other than Taylor and Francis.

Free Artcle Access to corresponding authors

As corresponding author, you will receive free access to your article on Taylor & Francis Online. You will be given access to the My authored works section of Taylor & Francis Online, which shows you all your published articles. You can easily view, read, and download your published articles from there. In addition, if someone has cited your article, you will be able to see this information. We are committed to promoting and increasing the visibility of your article and have provided guidance on how you can help.

Responsibility of the Board

Board of Editors, Editorial Advisory Board and the Publisher Adenine Press will have discharged responsibility once an article is published. They are not responsible for any or part of statements and claims made by authors in their articles.

It is understood that the communicating author, collectively represents all authors of an article, and that he/she has obtained permission form all authors to communicate the article in their behalf. Adenine Press, the Journal of Biomolecular Structure and Dynamics or its Board is not responsible, for any negligence or omissions by the communicating author.

Optional Open Access Policy for JBSD

Taylor & Francis Open Select provides authors or their research sponsors and funders with the option of paying a publishing fee and thereby making an article permanently available for free online access – open access – immediately on publication to anyone, anywhere, at any time. This option is made available once an article has been accepted in peer review. Full details of our Open Access programme