Instructions

Download a copy of the Instructions to Authors in PDF format.

Instructions to Authors

Subjects Covered

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.

A single PDF file of the complete manuscript (including text, tables and figures) can be emailed as an attachment to any one of the members of the Board of Editors, listed below, or directly to the Editor-in-Chief. This Journal uses PDF files to complete the review process. The PDF must be a light file and the author should embed the fonts; otherwise the reviewers may not be able to see special characters and symbols. If you are unable to make a PDF file, you can supply the complete manuscript as an MSWORD.DOC file. In creating the MSWORD.DOC file, if you experience problems in inserting your figures, supply the figures separately as .jpg, .tif or.eps formats. If the manuscript is submitted with separate files for figures, send the manuscript and figures only to the Editor-in-Chief.

The authors must also supply the editor, the names, postal address, and emails of five possible referees for the paper.

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
HHMI, Columbia Univ., USA
fone: 1 212 851 4655 fx: 1 212 851 4650
rr2213@columbia.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

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

Editorial Offices Where the Manuscripts
Can Be Submitted

If a manuscript originates from a particular country, it does not necessarily mean that the manuscript should be submitted to the Editor in that country. Authors have the freedom to submit to any one of the editors. If the manuscript is submitted to an Editor other than the Editor-in-Chief, please forward a copy of the covering letter to the Editor-in-Chief at the time of submission. If the manuscript is submitted with separate files for figures, send the manuscript and figures only to the Editor-in-Chief.

The Editors reserve the right to redirect the manuscripts to other members of the Board of Editors or send to the Editor-in-Chief to assign an appropriate Editor.

Review by Referees

All articles will be subject to review by expert referees to ascertain scientific soundness. Authors should suggest a slate of five possible referees. The editors may or may not employ the recommended referees. Please include complete mailing address, phone, fax and e-mail details of the suggested referees.

Revised Versions

Email the manuscript as an attachment to rhs07@albany.edu. Supply the complete manuscript as an MSWORD.DOC file. In creating the MSWORD.DOC file, if you experience problems in inserting your figures, supply the figures separately as .jpg, .tif or.eps formats. The figures must be at a resolution of 300 ppi (dpi) and must be at a size larger than the size at which they will be printed. In addition to the MSWORD.DOC file, also email a PDF of the revised manuscript.

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 and Special Characters

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.

Manuscript Organization

The manuscript may be arranged in the following manner: 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 the number in the reference section). This is because PubMed, Chemical Abstracts and Biological Abstracts use the abstracts from the Journal directly.

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. Figures are numbered using the Arabic system (i.e. 1, 2, 3 ...) and tables are numbered in the Roman manner (i.e. I, II, III ...).

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:

Title in upper and lower case
Authors and their affiliation. In the case of authors who originate from different institutions, please include a complete mailing address for each institution.
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.

References

References are numbered sequentially and the numbers must appear in parenthesis in the text, and without parenthesis in the reference section(see below). Books and journals are treated equally, their names and volume numbers appear in regular italic. Some examples of the arrangement of references (1-3) are given below. All journals should be abbreviated using standard abbreviations which are available at PubMed.

V. Righi, J. M. Roda, J. Paz, A. Mucci, V. Tugnoli, G. Rodriguez-Tarduchy, L. Barrios, L. Schenetti, S. Cerdan & M. L. Garcia-Martin. NMR Biomed 22, 629-637 (2009).
A. Thakar, J. D. Parvin & J. Zlatanova. J Biomol Struct Dyn 27, 399-406 (2010).
C. M. Rocha, A. S. Barros, A. M. Gil, B. J. Goodfellow, E. Humpfer, M. Spraul, I. M. Carreira, J. B. Melo, J. Bernardo, A. Gomes, V. Sousa, L. Carvalho & I. F. Duarte. J Proteome Res 9, 319-332 (2010).

Download a sample reference page in JBSD

If your references are in an EndNote Library, please download the JBSD Style Plugin from link below and place it in your EndNote Style Folder, and relaunch EndNote to format the References to JBSD style which will now appear in the style manger.

JBSD Style Plugin for EndNotes

If a manuscript that does not follow the above guidelines for the reference section is received, it will be returned back to the author to correct the formatting before processing the paper. This unnecessarily causes delays.

Footnotes

For page 1 to identify author affiliation, footnotes 1, 2, 3 .... appear as superscripts. All subsequent footnotes appear in lower case alphabet (a, b, c .....) 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 start a new paragraph, similar to the one below, under the title "Supplementary Material" and insert the paragraph towards the end of the manuscript preferably before the acknowledgement section.

Supplementray material dealing with ----------------- is available at no charge from the authors directly; the supplementary data can also be purchased from Adenine Press for US $50.00. It can also be downloaded free of charge from the author's server at the URL --------------.

Equations

Mathematical equations should be clearly created and numbered in the text. The number should appear in square brackets, i.e., [ ], to distinguish them from reference numbers. They must be clearly visible in black in the hardcopy. Equations can be created using Words equation editor.

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. However, there may be charges for certain special services such as color printing.

Color Printing Charges

Color printing charges continue to remain high for this Journal because it is printed and bound in US plants located in New York. Authors are charged a minimum of 20-25% of the charges of color printing, and the Journal pays the remaining 75-80%. On the average this will come to US dollars 350 to 900 for 2 to 5 regular size color figures.The use of color in articles dealing with biological structure and dynamics has become so routine that this Journal no longer wish to covert color renditions into black and white and compromise on the quality of the presentation.

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 of articles accepted for publication in the Journal must sign a standard copyright transfer form. Authors are completely responsible for obtaining the permission to reproduce materials such as figures, copyrighted text etc by a publisher/agency other than Adenine.

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

For a detailed write up of JBSD Open Access including forms please visit the linK:

JBSD Open Access

When an article is published under "Open Access," it , in full text, full image, and searchable form, becomes universally available in digital form, free of charge to anyone in the world. The authors, the publisher, and the right holders grant the right to use, reproduce, and disseminate the work in digital form to all users.

The availability of full text articles in fully searchable form under open access enables the various internet search engines and crawlers to go through the article and index the results. This may increase the probability of other researchers becoming aware of the work.

Open access treats the cost of publication as part of the research project, and it is estimated that the current cost is US $1,500 per article.

The authors of articles in JBSD may elect to have their articles published under "Open Access," provided the cost of publication (US $1,500) is paid in advance. This policy applies to articles already published or for future submissions. If Open Access Option is not exercised, the articles will be published in the traditional manner, in print and online versions.

When an article is published in JBSD under Open Access, the following will happen: