Proteins: Structure, Function, and Bioinformatics
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Edited By: Bertrand Garcia-Moreno
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ISI Journal Citation Reports © Ranking: 2013: 32/74 (Biophysics); 139/291 (Biochemistry & Molecular Biology)
Online ISSN: 1097-0134
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Instructions For AuthorsAll PROTEINS manuscripts must be submitted online via ScholarOne Manuscripts at http://mc.manuscriptcentral.com/prot. Please do not submit hard copies.
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Types of Articles
PROTEINS: Structure, Function, and Bioinformatics accepts six different types of manuscripts, all of which are peer-reviewed:
RESEARCH ARTICLE: This is the main avenue for publication of original research. Most of the articles published in any volume of PROTEINS are in the form of Research Articles. This form of publication is intended for reports of substantial research that make clear contributions that advance a field or a problem. We discourage submission of Research Articles based on material that is more appropriate for an archival journal.
SHORT COMMUNICATION: Research reports can also be submitted in the form of a Short Communication. These are reserved for short reports of highly important and noteworthy findings. A Short Communication cannot be longer than 4 printed pages.
REVIEW: Reviews contribute critical assessment of interesting and important problems or fields. Authors wishing to submit reviews are encouraged to contact the Editor-in-Chief for approval prior to submission. All Reviews in PROTEINS are peer-reviewed.
PERSPECTIVE: Previously known as Research Commentary, the Perspectives section is intended for opinion pieces in a range of styles. The goal of this section is to foment presentation of controversial ideas, critical evaluation of concepts, idiosyncratic viewpoints, and challenges to ideas. Didactic pieces and historical and biographical accounts will also be considered.
STRUCTURE NOTE: This type of report was created to provide an avenue for dissemination of structures determined by x-ray crystallography or solution or solid-state NMR spectroscopy. The goal of a Structure Note is to document a new structure or another interesting structural finding. Some Structure Notes can be followed up with a more comprehensive description of biological impact, published at a later date. Structure Notes are a useful forum for structures determined under structural genomics initiatives and other structural biology projects. They are expected to contribute novel structural or biological insight. Structure Notes cannot be longer than 4 printed pages (3500 words, not including the Abstract and References). Specific instructions for the format of Structure Notes are presented below. We discourage submission of Structure Notes describing structures that are already very well represented in the PDB, unless the structure contributes an exciting new finding, or important biological/biochemical insight.
Original submissions: First submissions of Research Articles and Reviews should be submitted as a single PDF document that includes title page, abstract, text, references, figure legends, tables and figures (in that order). The manuscript should conform to the format described in the instructions for manuscript preparation, below. For original submissions of Short Communications, Perspectives and Structure Notes must be submitted with production-ready files as described in the guidelines for revised submissions below.
Revised submissions: All revised manuscripts, as well as first submissions of Short Communications, Perspectives and Structure Notes, must be submitted with production-ready files. Carefully follow the instructions below to ensure that, if your manuscript is accepted, it will be published as quickly as possible. The manuscripts must also adhere to the format described in the instructions for manuscript preparation, below.
1. Submit your text file in .DOC or .RTF format.
2. The text document should include the title page, abstract, text, references and figure legends. Do not embed figures or tables in this document.
3. Designate this file as "Main Document" in the File Designation field when you upload it to ScholarOne Manuscripts.
1. Create tables as text files and save in either .DOC or .RTF format.
2. Designate this file as "Table" in the File Designation field when you upload it to ScholarOne Manuscripts.
1. Submit your figure files in .TIFF or .EPS format. After the files complete the upload process, label the figures by placing the figure number and figure legend in the Caption/Legend box for each figure. This should be done in addition to including a figure legend in your text file. Authors are also encouraged to use the file tags option when uploading image files in order to take advantage of the linked HTML features of ScholarOneManuscripts. All panels in a multi-panel figure (example: Figure 1A, 1B, 1C, etc.) must be submitted within a single file (example: Figure 1).
2. To ensure that your digital graphics are suitable for print purposes, please go to RapidInspector at http://rapidinspector.cadmus.com/zwi/index.jsp. This free, stand-alone software application will help you to inspect and verify illustrations right on your computer.
3. Vector-based figures (e.g., figures created in Adobe Illustrator) should be submitted in EPS format.
4. To ensure ease of legibility for reviewers as well as the highest print quality, TIFF and EPS files must be submitted according to the following minimum resolutions:
a. 1200 dpi (dots per inch) for black and white line art (simple bar graphs, charts, etc.)
b. 300 dpi for halftones (black and white photographs)
c. 600 dpi for combination halftones (photographs that also contain line art such as labeling or thin lines)
5. In addition to the above resolution guidelines, color figures must be submitted in CMYK colorspace. Do not submit color figures as RGB. This color space does not reproduce well for print production.
6. Designate this file as “Image” in the File Designation field when you upload it to ScholarOne Manuscripts.
Instructions for Submitting LaTeX Files
1. First, always upload the main body of the TeX/LaTeX document first (i.e. the file ending with ".tex") using the file designation "Main Document" for your TeX/LaTeX document.
2. Then upload each file that is a part of the LaTeX file needed for processing using the file designation “TeX/LaTeX Suppl Files”.
a. Be sure to upload all style sheets that are a part of the document.
b. All images must be EPS files in order for the file to properly format.
3. All files referenced by the main TeX/LaTeX document should be designated as “TeX/LaTeX Suppl Files”. Of note, if your tables and/or figures that are NOT referenced by the main TeX/LaTeX document, you should submit the figure(s) in .tif or.eps, and the table(s) in .doc format using the file designation “TeX/LaTeX Suppl Files”.
4. Lastly, you should submit the entire manuscript in PDF format (including text, figures, and tables) using the file designation “Main Document”.
Authors may submit Supporting Information for their articles to be posted in the electronic version of the journal. Instructions for preparation of Supporting Information are provided below. These materials must be submitted online using the File Designation “Supplementary Material for Review.” Supporting text, tables and figures must be in PDF format. The only exceptions are audio and moving image files, which should be submitted in .mov or .mp3 format. See the Instructions for Preparation of Supporting Material for further instructions.
Instructions for Manuscript Preparation
For Structure Notes please follow the special guidelines listed under “Instructions for Preparation of Structure Notes”. Please note that for all reports of new crystallographic structures, coordinates and structure factors should be deposited in the Protein Data Bank at the time of manuscript submission. The PDB id(s) should be included in the text. These data must be released upon publication of the accepted article (available on-line in EarlyView). Authors should note that the PROTEINS Editorial Board encourages release of coordinates and structure factors at the time of PDB deposition. Coordinates and structure factors might be requested from authors as part of the review process.
1. When submitting via ScholarOne Manuscripts, authors must provide the names, e-mail addresses, and institutions (affiliation) of five possible reviewers and two preferred Editors. Options are also provided for designating names of persons that authors prefer not to review or edit their paper. A brief explanation for exclusion of reviewers is suggested. The Editorial Office will refrain from assigning any person listed as “non-preferred”. Authors should note that preferred Editors and Reviewers may not be available nor will these persons necessarily be assigned as Editors or Reviewers.
2. Authors should include a cover letter to the Editor-in-Chief with the manuscript submission. This may be entered as plain text in the field provided, or uploaded as a .DOC, .RTF, or .PDF file.
3. All manuscripts must be in 12-point Times New Roman font, in single column and double spaced format.
a. Problems with use of English is increasingly a problem that precludes fair review of manuscripts. Authors that are not fully comfortable with English should have their manuscripts edited by a native English speaker. Authors in Japan may contact Wiley-Japan for a list of recommended services for checking and improving use of English. Please contact Yoko Kobayashi or A. Bocquet in the Wiley-Japan office by facsimile: 81 3-5689-7276 or by E-mail: email@example.com for more information. Please indicate the name of the journal clearly.
4. Number all pages in sequence, beginning with the title page.
5. 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.
Note that formats for Review articles are flexible. The text for all other manuscript types should conform to the following format.
Manuscripts that do not conform to the following format will be returned. The parts of the manuscript must appear in the following order:
The title page must contain the following information:
1. The full title of the manuscript. The title should be descriptive and representative of the material in the manuscript.
2. A short title of not more than 45 characters (including spaces).
3. Five to ten key words not used in the title that will adequately index the subject matter of the article.
4. The names and affiliations of all authors.
5. The institution at which the work was performed.
6. Complete contact information for the author responsible for correspondence:
c. E-mail address
This should summarize the purpose, methods, results, and major conclusions of the work. A 250 word limit will be strictly enforced.
Introduction, Materials and Methods, Results, Discussion, and Conclusion
1. The sections should be presented in the following order: Introduction, Materials and Methods, Results, Discussion, and Conclusion (if applicable). The Results and Discussion section can be combined into a single section when appropriate.
2. The manuscript should conform to standard scientific reporting style.
3. Sufficient data and information must be given so that the study can be replicated.
1. Cite references to published literature in the text numerically.
2. Provide full titles and complete page numbers for all works cited in the reference section.
3. Refer to the CBE style manual for the style of reference (see below for more information).
1. Figure legends should be as clear and concise as possible.
1. Indicate placement of all tables in the text with a citation (e.g., Table1, Table 2, etc.). When uploading tables and figures, use the same tags for file names in order to utilize HTML linking in the manuscript to these elements.
2.Tables must be numbered in order of appearance with Arabic numerals (e.g., Table 1, Table 2, etc.).
a. A legend must accompany each illustration, and tables must have titles.
b. All abbreviations used must be defined.
c. All lettering must meet professional standards and be legible after reduction in size.
1. Indicate placement of all illustrations in the text with a citation, i.e., (Fig.1). When uploading tables and figures, use the same tags for file names in order to utilize HTML linking in the manuscript to these elements.
2. Label the figures by using the Captions/Legend box to insert the figure number (i.e. FIGURE 1) AND the figure legend for each figure uploaded. This will help reviewers identify each figure in the PDF version of the manuscript.
3. For figures with multiple parts, the figures must be submitted in the assembled form in which they would appear in the published paper.
4. Figures must be submitted in the size (or close to it) in which they will appear in print.
5. Minimize the number of figures.
Color Figure Preparation
1. For best reproduction, bright, clear colors should be used.
2. Dark colors against a dark background do not reproduce well; please place your color images against a white background wherever possible.
3. 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. Parallel-viewing pairs are preferred. Authors who choose to submit cross-eyed pairs must specify this feature in the legend.
4. Follow resolution guidelines listed above under “File Format Instruction for Online Submission.”
Color Reproduction Charges
Color printing is free for one color figure and $250 for each additional color figure. Figures can be printed in black and white and appear online in color (as submitted) at no charge. You will receive a Color Charge form, post-acceptance, to enable you to make your color figure selections.
Authors may nominate figures (or portions thereof) from their manuscript to be used as a cover illustration for the print issue of PROTEINS. Include a request in your cover letter and upload your image using the File Designation “Supplementary Material Not for Review. Name your figure file “Cover Nomination”.
Instructions for Preparation of Supporting Information
Tables and Figures in Supporting Information should be labeled using the prefix S before the number (e.g. Table 1 in Supplementary Information should be labeled Table S1, Figure 1 in Supporting Information should be Figure S1). References are not allowed in the Supporting Information. All references should be included in the References section of the main text. Preparation of Tables and Figures should follow the same guidelines described above for the main text.
The length of a Structure Note cannot exceed 4 printed pages (4000 words). The format for a Structure Note consists of: (i) Title Page (described above under Instructions for Manuscript Preparation). (ii) Abstract of 100 words maximum, (iii) Introduction stating clearly the protein/gene name and their identifiers in the appropriate databases, if relevant (e.g. Uniprot, Pfam, COG, etc). Authors must provide a relevant sequence or structure-based multiple alignment to place the new structure in the context of homologous sequences. The residue numbering of the protein along with its secondary structural elements should be included in the sequence alignment figure. (iv) Materials and Methods. (v) Results and Discussion section will include a concise description of the structure, including its secondary structural elements, topology, and oligomerization state. Authors should also identify any similar protein structures in the Protein Data Bank, and briefly discuss any biological/functional/mechanistic implications that can be gleaned from the structure. Any novel/specialized techniques used in the work can be briefly described in this section. (vi) References, not to exceed 15. (vii) Tables - one table with structural parameters is allowed. The table must have a title. (viii) Figure Legends. (ix) Figures. No more than two composite figures are allowed. The figures should be prepared in the size in which they will appear in print. Figures with more than one panel must be assembled as they will appear in print. (x) Supplementary Information is allowed. The Supporting Information can include a complete description of the expression, purification, NMR data acquisition, and structure determination methods used in the study. Supporting figures and tables relevant to the study can also be included to describe experimental data used to establish the oligomerization state the protein (e.g. light scattering or NMR relaxation). This data should be included in the data. Supplementary Figures and Tables can also included to report NMR assignment connectivity information, nuclear relaxation data, phylogenetic tree, etc. The text a Structure Note must be no more than 3500 words long, excluding the Abstract and References. Note that all other general guidelines for the preparation of Research Articles also apply. Note that the charges for Structure Notes are $300 for the first page and $200 for each additional page. Included in this price are 100 reprints of the article.
Public data deposition is described individually for crystallographic and NMR structures below. Data deposited in either PDB or in the BioMagResDB must be released upon publication of the accepted article (available on-line in EarlyView). The electronic version will contain a link to the relevant entry in the Protein Data Bank and BioMagesDB. The Editorial Board of PROTEINS encourages release of coordinates and structure factors at the time of PDB deposition. Coordinates and structure factors might be requested from authors as part of the review process.
A good summary of structure validation can be found in the article by Gerard Kleywegt, Acta Cryst. (2000) D 56, 249-265.
For all crystallographic studies, coordinates and structure factors should be deposited in the Protein Data Bank at the time of manuscript submission. The PDB id(s) should be included in the text.
For all crystal structures the following data must be summarized in one Table:
1. The space group, unit cell dimensions, the Wilson plot B value for the data and the effective resolution.
2. The effective resolution should be described clearly by quoting the following crystallographic indicators for the entire data set and for the highest resolution shell (shown in parentheses): (i) the completeness of the data set; (ii) the internal agreement of the data (Rmerge); (iii) the average I/σ (I)value; (iv) the redundancy of the collected data (reflections measured divided by the number of unique reflections).
3. The absolute number of unique reflections observed (after merging), number of measured reflections (before merging) and the number of unique reflections used in the Rfree set.
4. If crystallographic twining was detected, the twin law and the twin percentage should be clearly shown.
5. For the refinement statistics, the crystallographic R-factor and the corresponding Rfree should be quoted along with the number of molecules of each type that are present in the asymmetric unit. The total number of atoms in the biological molecules related by non-crystallographic symmetry must be given, as well as the number of ions, water molecules, and ligands. For each of these classes of molecules the average B factors should be given. The RMS deviations from ideal geometry (and ideally the RMSZ score reported by modern refinement software) should be given for bonds and angles). In the cases of TLS refinement the number of TLS bodies should also be included in the table.
6. For validation we strongly encourage all authors to use the free MolProbity software that is available on the web (http://molprobity.biochem.duke.edu), Davis et al (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35: W375-W383). The following indicators are required to be tabulated: (i) the percentage of residues that are outliers in the Ramachandran plot, (ii) the percentage of residues that are in favored regions of the Ramachandran plot, and (iii) the percentage of rotamer outliers.
The Methods section should provide adequate details regard the steps followed in constructing the model and refining the structure, with appropriate citations to all software used:
1) For molecular replacement solutions, the way that the search model was constructed should be explained, quoting the PDB IDs of the search model(s).
2) For heavy atom phasing, details on each dataset used should be provided as additional columns for all items in sections 1-4 of the main Table described above. However, the completeness (i) and the redundancy (iv) should be quoted also treating Friedel pairs as separate observations (as items v and vi). Indications about the initial map quality can be given in the text.
3) The history and salient details of the refinement methods employed: the type of restraints used, a description of how the thermal parameters were treated, and how solvent sites were selected and handled during refinement.
Any structural features that are considered somewhat unusual should be described. Examples include: cis-peptide bonds, unoccupied volume inside the protein, buried ionizable groups that are not involved in salt bridges or reasonable hydrogen-bonding environments, unusual locations of glycine and proline residues, and unusual distribution of polar and hydrophobic groups within the molecule.
Structures from NMR spectroscopy
A composite Figure may include (i) multiple sequence alignment, and (ii) stereoview of a ribbon representation of the structure. All secondary structural elements and the N- and the C-termini of the protein should be clearly labeled on the structure. Other sub-figures or a second figure could include other structural information, such as a depiction of the structural ensemble, conserved surface and/or electrostatic surface images, or comparison with similar or homologous protein structures. A stereo image of a superimposed ensemble of 10-20 conformers must be included either as a subfigure or as a Supporting Figure. A Table of structural statistics describing the overall quality of the structure should be included, and it can be submitted as a Supporting Table. It should include summaries of NMR assignment completeness statistics, a summary of constraint types and their distributions, summaries of constraint violations, backbone and heavy atom RMSDs (with ordered-residue ranges defined), deviations from ideal geometry, and other structure quality statistics (e.g. Ramachandran, ProCheck-NMR, and/or MolProbity statistics). Deposition of data: In addition to the atomic coordinates, the list of assigned chemical shift, the list of NOESY peaks (if appropriate), and the complete list of experimental constraints data used in the last round of refinement must be deposited with the PDB and BMRB. The PDB and BMRD identifier codes must be provided in the main text. Hydrogen bonding patterns within the protein should be described, with particular attention to unsatisfied buried main chain hydrogen bonds. A good summary of protein NMR structure validation can be found in the article by Bhattacharya et al. PROTEINS (2007) 66: 778-795. Any structural features that are considered somewhat unusual should be described.
In addition to the atomic coordinates, the following data should also be deposited with the PDB and BMRB: list of assigned chemical shifts, list of NOESY peaks (if appropriate), and complete list of experimental constraints used in the last round of refinement. The PDB and BioMagResDB identifier codes must be provided in the main text.
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 (www.wwpdb.org): RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/pdbe), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu). The PDB ID must be included in the manuscript and entered into the designated field in the ScholarOne manuscripts upon submission. Authors must agree to release the atomic coordinates and experimental data when the associated article is published. Questions relating to depositions should be sent to firstname.lastname@example.org.
Authors are strongly 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 Online Library at www.wileyonlinelibrary.com .
The Genome Database (GDB)
Protein Databank (PDB)
Online Mendelian Inheritance in Man (OMIM)
Molecular Modeling Database (MMDB)
European Molecular Biology Laboratory (EMBL)
1. 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.
2. Please follow the instructions in the Database Linking Submittal Form, and submit a copy of that form with your manuscript.
3. 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.
4. The publisher will not submit new information to the databases. Incorrect information will result in the omission of hypertext links in the article.
5. 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.
6. 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.
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.
2. Voet D, Voet JG. Biochemistry. New York: John Wiley & Sons; 1990. 1223 p.
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.
4. Bio-Xplor, Version 1.0. New York: Biostructure Inc.; 1991.
In order to expedite the publication and online posting of articles in Wiley Online Library, PROTEINS: Structure, Function, and Bioinformatics 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 and problems.
Preprints of accepted manuscripts will be assigned a DOI number and posted to Wiley Online Library within a week of being sent out for production. Once the manuscript has been proofed and typeset, the preprint will be removed from Wiley Online Library and replaced with the most current version in EarlyView.
Reprints can be purchased at https://caesar.sheridan.com/reprints/redir.php?pub=10089&acro=PROT
Disclaimers, Rights and Responsibilities
All Manuscripts submitted to PROTEINS: Structure, Function, and Bioinformatics must be submitted solely to this journal, and may not have been published in another publication of any type, professional or lay. Manuscripts published previously in the proceedings of a scientific meeting, or in a journal such as Nature Precedings, should not be submitted to PROTEINS .
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Note to NIH Grantees
Pursuant to NIH mandate, Wiley-Blackwell will post the accepted version of contributions authored by NIH grant holders to PubMed Central upon acceptance. This accepted version will be made publicly available 12 months after publication. For further information, see www.wiley.com/go/nihmandate
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