In taking a step toward expediting the publication process, Proteins: Structure, Function, and Genetics is now pleased to offer web-based submission and peer review.
To submit your manuscript online, please:
1. Prepare your manuscript and illustrations in appropriate format, according to the instructions given at http://prot-wiley.manuscriptcentral.com/ under the "Instructions and Forms" button. Please also be sure that your paper conforms to the scientific and style instructions of the journal.
2. If you have not already done so, create an account for yourself in the system at the submission site, http://prot-wiley.manuscriptcentral.com/ by clicking on the "Create an Account" button. To monitor the progress of your manuscript throughout the review process, just login periodically and check your Author Center.
3. Please be sure to study the Instructions and Forms given at the site carefully, and then let the system guide you through the submission process. Online help is available to you at all times during the process. You are also able to exit/re-enter at any stage before finally "submitting" your work. All submissions are kept strictly confidential. If you have any questions, do not hesitate to contact us at edsupport@wiley.com.
Structure Notes. Structure Notes are one-two page articles describing a novel protein structure. The electronic version will contain a link to the relevant entry in the Protein Data Bank. The text of each article must not exceed 6,000 characters. One table containing structure parameters and one figure may be submitted. The figure may be reproduced at 3" ?2.5" (width by length). The Production Department will reduce any figure which is larger than these dimensions to fit the allotted space. Please include a table title or figure legend.
The page charges for this section are $300.00 per one page article, $500.00 per two page article. If the specifications above are not followed additional charges may be levied. Included in this price are 100 reprints of the article.
Restriction on Submission of Serial Manuscripts. Effective immediately, authors seeking to submit two or more manuscripts that form a series must have advance and written authorization from the Editor-in-Chief. We regret inconveniencing our authors by establishing this new obstacle; however, it has become increasingly difficult to handle the serial manuscripts. It is frequently impossible to find managers and/or reviewers to review a set of manuscripts. If manuscripts are distributed to different managers and/or reviewers, we receive inconsistent recommendations, as those reviewing are not able to make a fair assessment without having read the entire series to see the 'complete picture'. Permission to submit a series of more than two manuscripts will very rarely be granted.
Instructions for Manuscript Preparation
Manuscripts. Authors must provide the names, telephone numbers, fax numbers, e-mail addresses, and full addresses of four possible reviewers in order to decrease manuscript processing time. Space is also provided to list those referees that the authors prefer not to review. Authors must also include a cover letter to the Editor-in-Chief with the manuscript submission. All manuscripts must be typewritten, double spaced, in English. Authors in Japan please note: Wiley-Japan can provide authors in Japan with a list of recommended services to check and improve the English in their papers BEFORE SUBMISSION. Please contact Masayo Kobayashi in the Wiley-Japan office by Fax (03) 3556-9763 or E-mail: editorial@wiley.co.jp for more information. Number all pages in sequence, beginning with the title page. Follow the guidelines in CBE Style Manual Committee. CBE style manual: a guide for authors, editors, and publishers in the biological sciences. 5th ed. rev. and expanded. Bethesda, MD: Council of Biology Editors, Inc.; 1983. The text should conform to the following format:
Title Page. This must contain the complete title of the manuscript, names and affiliations of all authors, institution at which the work was performed, name, address and telephone, telefax numbers, and e-mail address of author responsible for correspondence, a short title of not more than 45 characters (including spaces), and five to ten key words not used in the title that will adequately index the subject matter of the article.
Abstract. This should summarize the purpose, methods, results, and major conclusions of the work in fewer than 250 words.
Introduction, Materials and Methods, Results, Discussion, and Conclusion. These should conform to standard scientific reporting style. Sufficient data must be given so that the study can be replicated. Where appropriate, the Results and Discussion Sections may be combined.
References to published literature should be cited in the text numerically. It is important to provide full titles and complete page numbers of all works cited in the reference section. Please refer to the CBE style manual for the style of reference.
Wiley's Journal Styles Are Now in EndNote
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Download Reference Style for this Journal: If you already use EndNote, you can download the reference style for this journal.
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Journal:
1. King VM, Armstrong DM, Apps R, Trott JR. Numerical aspects of pontine, lateral reticular, and inferior olivary projections to two paravermal cortical zones of the cat cerebellum. J Comp Neurol 1998;390:537-551.
Book:
2. Voet D, Voet JG. Biochemistry. New York: John Wiley & Sons; 1990. 1223 p.
Book Chapter:
3. Gilmor ML, Rouse ST, Heilman CJ, Nash NR, Levey AI. Receptor fusion proteins and analysis. In: Ariano MA, editor. Receptor localization. New York: Wiley-Liss; 1998. p 75-90.
Electronic Media:
4. Bio-Xplor, Version 1.0. New York: Biostructure Inc.; 1991.
Tables and Illustrations. Indicate placement of all tables and illustrations in the text with a citation, i.e., (Table I). Tables must be numbered in order of appearance with Roman numerals; illustrations with arabic numerals. A legend must accompany each illustration, and tables must have titles. All abbreviations used must be defined. All lettering must meet professional standards and be legible after reduction in size.
Identify all illustrations by affixing a gummed label on the back listing the number of the illustration, first author's name, short title of the manuscript, and an arrow indicating the top. Do not submit original recordings, radiographic plates, or artwork.
Color Figure Preparation. For best reproduction, bright, clear colors should be used. Dark colors against a dark background do not reproduce well; please place your color images against a white background wherever possible. Unless otherwise arranged with the Editor, stereo pairs will be printed to a scale that yields a separation of 55-60 mm between corresponding points in the left and right images. Each stereo pair should be provided in a pre-mounted or composite form; do not submit "cross-eyed" pairs.
Color Reproduction Charges. One color page per article will be considered by the Editor-in-Chief for reproduction free of charge, subject to the recommendations of reviewers and the Associate Editors. Additional color pages will be published at a nominal charge to authors of $500 for each additional page thereafter.
Cover Illustration. Authors may submit black-and-white or color figures for cover illustrations. These figures must be used and explained in the author's manuscript. If a color figure is selected for the cover illustration, it will be printed in the article without charge to the author.
Software and format. All illustration files should be in TIFF or EPS (with preview) formats. Do not submit native application formats.
Resolution. Journal quality reproduction will require greyscale and color files at resolutions yielding approximately 300 ppi. Bitmapped line art should be submitted at resolutions yielding 600-1200 ppi. These resolutions refer to the output size of the file; if you anticipate that your images will be enlarged or reduced, resolutions should be adjusted accordingly.
File names. Illustration files should be given the 2- or 3-letter extension that identifies the file format used (i.e., .tif, .eps).
Database Linking. Authors are encouraged to submit genetic and protein database information with their manuscript for the databases listed below and a hypertext link will appear in the online version of the article, via Wiley InterScience at www.interscience.wiley.com.
The Genome Database (GDB)
Protein Databank (PDB)
Genbank
Online Mendelian Inheritance in Man (OMIM)
Molecular Modeling Database (MMDB)
Entrez Genomes
Entrez Proteins
European Molecular Biology Laboratory (EMBL)
SpecInfo
ExPasy
To create hypertext links authors must supply the gene name as it appears in the article, the database where the record appears, and the database specific identification number or name. Please follow the instructions in the Database Linking Submittal Form, and submit a copy of that form with your manuscript.
It is the responsibility of the author(s) to ensure that the database information that is provided with the manuscript is correct and up to date. The publisher will not submit new information to the databases. Incorrect information will result in the omission of hypertext links in the article.
For those articles containing gene and protein sequence information with a corresponding database record (see list of databases) hyperlinked database queries will be added to the online version for the full-text HTML version of the journal. The hypertext links will appear in the Special Content Links section of the Abstract page, the text of the abstract and throughout the full text of the article.
Supplementary Online Material. Authors may submit supplementary material for their articles to be posted in the electronic version of the journal. There are no restrictions on file types, however please keep in mind that the more universal the file type the more accessible it will be to the community. All supplementary material must be submitted online as "Supplementary Material" for peer review.
Electronic Proofing. In order to expedite the publication and online posting of articles in Wiley InterScience, PROTEINS: Structure, Function, and Genetics now offers electronic proofing. Corresponding authors with e-mail addresses will be sent page proofs (and paperwork, such as reprint order forms) in .pdf format via e-mail. Please follow the instructions in the e-mail; contact names and numbers are given for questions, problems, or if an author wishes to receive a paper proof. A fax cover form with the Production Editor's information is also provided for authors to fax their corrections. Please notify us of your preferred proof delivery method when submitting your final manuscript to the editorial office. Indicate in your cover letter your page proof choice: ELECTRONIC (.pdf) or TRADITIONAL (paper).
Criteria for Evaluating and Reporting Macromolecular Structures
The following text follows closely upon that developed by Charlie Bugg for Acta Crystallographica. A few changes and additions have been made.
At the IUCr meeting in Bordeaux, there was a Discussion Session directed at defining criteria for reporting structures of biological macromolecules. From this Discussion Session, a set of proposed criteria was developed by the Commission on Journals and the Commission on Biological Macromolecules. These proposed criteria were circulated widely, and have now been revised based upon comments received from the crystallographic community. It is clear that the macromolecular crystallography field is at a stage where standards are evolving rapidly. Until there is a general consensus regarding specific criteria that apply broadly to macromolecular structural analyses, it would be a mistake to adopt rigid rules and requirements to be imposed on authors, referees and editors. Thus, the criteria that have been developed at this stage might be considered as guidelines for helping to assess the reliability and completeness of macromolecular structural reports.
A. For all structural studies, coordinates should be deposited in the Protein Data Bank at the time of publication, in accordance with the guidelines developed previously by the Commission on Biological Macromolecules. The deposition code number should be provided with the manuscript. Proteins strongly encourages that these coordinates be available immediately. However, a delay of one year in the release date may be permitted if an explanation is provided in writing. Deposition of structure factors is strongly encouraged but not required.
B. Preliminary structures determined by isomorphous replacement or molecular replacement methods: It is expected that protein structures will normally be refined at the appropriate resolution before they are submitted for publication. In those exceptional cases when unrefined structures are reported, the authors should justify not refining their structures by crystallographic methods. It is generally recognized that criteria for evaluating unrefined structures determined at medium to low resolution must be extremely flexible. Basically, the burden is on the authors to provide adequate experimental details to convince referees that the interpretation is correct, within the resolution of the analysis. In many cases, portions of the criteria listed below for evaluating refined structures would be appropriate for describing lower resolution analyses. If heavy atom derivatives were used, sufficient data should be provided for evaluating the quality of these derivatives. The fit of the model to the electron density maps used to determine the structure should be shown or described by quantitative indicators, such as real space residuals. Various pitfalls and criteria that have proved useful in evaluating low to medium resolution structures were recently summarized by Carl Branden and T. Alwyn Jones (Nature 343: 687-689, 1990).
C. For refined structures, the data submitted will depend somewhat upon the effective resolution of the analysis. In most cases, it would be helpful to include the following:
1. Effective resolution should be described clearly by giving the percentage of data recorded in the various resolution ranges; the internal agreement of the data in each of these ranges; the percentage of data considered observable in each of the resolution ranges, along with the specific criteria that were used to select observable data; and the average I/
(I) value for each range.
2. The crystallographic R-index (
||Fobs|-|Fcalc||/|Fobs|) should be tabulated as function of resolution. For each shell, the number and fraction of reflections observed should be given, as well as the number actually used in the calculation of the R-index. Any selection criteria should also be provided. The R-index should be computed with and without solvent included.
3. A final Ramachandran plot or related conformational analysis should be given with the favorable energy regions indicated. Distributions of 
1, 2 values for sidechains might be presented, along with an analysis of deviations from expected minimum energy ranges. An indication of the range of the peptide angle 
should also be given.
4. The average B-values should be plotted or given for individual residues,including the average values for mainchain atoms and the average values for the sidechain atoms. In addition, it may be worthwhile to include the rms deviations in B-values within each residue's mainchain and sidechain atoms.
5. Adequate details should be provided regarding the steps followed in constructing the model and refining the structure. The number of solvent atoms should be given, along with information regarding solvent B-values, and the approach that was used to identify solvent sites. The report should include the history and salient details of the refinement methods employed, including the resolution ranges that were used at various stages of refinement; the restraints used; a description of how the thermal parameters were treated; and how the solvent sites were selected and handled during refinement. It should be clear if van der Waals' distances were restrained, either explicitly or by energy minimization methods.
6. Hydrogen bonding patterns within the protein should be described. The number of hydrogen bond donors that are not involved in hydrogen bonding should be given, with particular attention to unsatisfied buried mainchain H-bonds.
7. Deviations of bond lengths, bond angles, and planes from ideal geometries should be given. Close intramolecular and intermolecular van der Waals' contacts should be described. The character and stereochemistry of major crystal contacts should be discussed.
8. Any structural features that are considered somewhat unusual should be described. Examples include: cis-peptide bonds, unoccupied volume inside the protein, buried charged groups that are not involved in salt bridges or reasonable hydrogen-bonding environments, unusual locations of glycine and proline residues, and unusual distributions of polar and hydrophobic groups within the molecule.
9. (The following is a Proteins-specific requirement). The free R-index is not a precisely defined quantity. For example, the free R-index is sometimes effectively refined by adjusting the refinement protocols so that it is reduced. It is thus difficult to required that it be reported. However, we encourage authors to report it and to describe under what conditions it was obtained.
Labels. Label all disks with your name, the file names, formats, and compression schemes (if any) used. Hard copy output must accompany all files.
Copyright Transfer Agreement
Database Linking Submittal Form
All Manuscripts submitted to PROTEINS: Structure, Function, and Genetics must be submitted solely to this journal, and may not have been published in another publication of any type, professional or lay. Manuscripts (including original figures) that are not accepted for publication will not be routinely returned to authors. Upon acceptance of a manuscript for publication, the author will be requested to sign an agreement transferring copyright to the publisher, who reserves copyright. No published material may be reproduced or published elsewhere without the written permission of the publisher and the author. The journal will not be responsible for the loss of manuscripts at any time. All statements in, or omissions from, published manuscripts are the responsibility of the authors, who will assist the editor by reviewing proofs before publication. Reprint order forms will be sent with the proofs.
Production Questions
Marc Nadeau
Phone: 201-748-6716
Fax: 201-748-6052
E-mail:mnadeau@wiley.com
