Submissions

Author Guidelines

Download author guidelines in PDF

1. Journal of Molecular Docking publishes various scientific articles in the field but not limited to Pharmacy, Chemistry, Physics, Bioinformatics, and other areas that utilize molecular docking methods, which have never been published in other scientific publication media.
2. Manuscripts published in the form of a preprint on several platforms such as arXiv, Preprints, SSRN, and ResearchGate are welcome to publish.
3. The manuscript is written in English (Can be English American or British as long as it is consistent and does not mix the two) with Book Antiqua font 11 pt, two-column, density 1.08 spaces, spacing after 8 pt, on A4 paper with a top-down and right-left margins of 2.54 cm. Templates for the Journal of Molecular Docking are available HERE (ORA & SC) and HERE (LR & EO), while the template for the title page is available HERE.
4. The manuscript is typed with the MS-Word program using the provided template and saved in .doc or .docx format.
5. The title page and manuscript is typed strictly with the following rules:
   a. The title: short and precise, written in English. The title length does not exceed 15 words.
   b. Authors: listed without mention of title or degree, under the name including the affiliation and complete address, and institutional email address and phone numbers of the corresponding author. The author's name, which consists of one word, must be repeated twice for first and last names. To an author with names of more than two words, the author's last name consists of only one word; the rest is written as the first name. The first author and the corresponding author must include ORCiD, while other co-authors are optional (but highly recommended)
   c. Abstract: written in English, which summarizes the article. The abstract is created in one paragraph, and the number of words is between 150-250 words without any citations with Book Antiqua font 11 pt, single column, and space 1. Points that must be listed in the abstract include the background, objectives, methods, results, conclusions, and keywords. At least three keywords are separated by a semicolon.
   d. Authors' contributions: All authors must have contributed significantly to the research. Contributions of each author are compiled based on CRediT - Contributor Roles Taxonomy (https://casrai.org/credit/). Divided into Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing - original draft, and Writing - review & editing.
   e. Introduction: Contains background, reasons for the importance of underlying research or hypotheses, general approaches and objectives of the study, and relevant literature review. The number of paragraphs is not restricted, but the contents must include background, objectives, positions on previous research, and the study's novelty. The little theoretical basis indirectly related to the article's contents could be had without sub-chapters required. Citations are numbered consecutively in the order of appearance in the text at the end of the sentence in superscript without brackets, for example, Text¹, Text^2,3, and Text^4-6.
   f. Method: Hardware and Software: State the hardware system (Type, Brand, OS, CPU) and all the software used, along with the version.
   Ligands: Explain the type, amount, and how the ligands used are obtained. Known ligands do not need to include their structure; simply mention their identity (PubChem CID, CAS number, etc.). The ligands in the form of a modified compound or a new chemical entity need to describe their two-dimensional structure along with the IUPAC name.
   Receptors: The receptors used are mentioned along with their PDB ID. The receptors obtained from the modeling results need to mention the software used and the source code.
   Docking protocol: The protocol used must contain a validation procedure. The docking protocols are described in full. If the protocol is adopted from previous research, it does not need to be written in full and only mentions its references.
   Assessment: The parameters used in assessing and ranking the test ligands of the docking results are clearly stated.
   The sub-chapters are written without numbering or bullets. For review articles, this section is replaced by the first chapter.
   g. Results and Discussion: At least contain three subjects (1) description of results, (2) interpretation or explanation of results, and (3) comparative of results with previous studies results. Suppose the subchapter's very length could be made sub-sub-chapters with Arabic numbering. The results can be in tables and figures with a serial number (Table used a sequence of Roman numerals and placed at the top, while figures using Arabic numeric sequence and placed in the below). For review articles, this section is replaced by the second chapter and so on.
   h. Conclusion: Made in a single paragraph without the citation, it contains the conclusion and suggestions for advanced research.
   i. Conflicts of interest: Contains information on possible authors' conflicts of interest. It should be as detailed as possible as provided in the ICMJE form as the standard authors' disclosures. Financial and personal relationships are easily identifiable, leading to bias in work. The authors should state that the authors have access to all the studies and that the sponsors have not interacted with the data or the work. Conversely, if the authors do not have a conflict of interest, simply write, "The authors have no conflicts of interest to declare that are relevant to the content of this article."
   j. Funding: Contains information on funding sources from research and the research contract number. If there isn't, simply write "None."
   k. Availability of data and material: Contains information on the availability of raw data on research results that the authors upload independently both on the open access repositories and other sources.
   l. Acknowledgments, Contain gratitude and appreciation for the parties involved in the research but not included in authorship. Include individuals who have assisted you in your study: advisors, financial supporters, or other supporters, i.e., Proofreaders, typists, and suppliers who may have provided materials. Do not recognize the names of one of the authors.
   m. References: The references are published within the last five years (the minimum percentage and a minimum number of references are different for each type of manuscript). Reference format using Vancouver style and suggested using a reference management application such as EndNote, Mendeley, Zotero, and other applications. 
6. All manuscripts must be submitted to the Journal of Molecular Docking Editorial Office using the OJS 3.1.1.2 Online Submission Service at the following URL address: http://journal.umpalangkaraya.ac.id/index.php/jmd/submission/wizard, where the author should first register as Author Role. If you have any problems with online submissions, please get in touch with the Editorial Office at jmd@umpr.ac.id or mohammadrizkifadhilpratama@umpr.ac.id. The Cover letter outlines the essential findings of the paper, and its significance should accompany the manuscripts submitted through the online submission interface.
7. Four types of manuscripts are acceptable for publication: Original Research Articles, Short Communication, Literature Review, and Expert Opinion. The authors determine the type of manuscript based on the content of each manuscript; editors only continue to type the manuscript that the authors have chosen. The general difference between original research articles and short communication lies in the length and depth of the manuscript's content.
   a. Original Research Articles: Written by at least two authors (preferably from different institutions). The manuscript contains a word count between 4,000 to 6,000 words. The number of references used is at least 20, with 60% coming from the last five years.
   b. Short Communication: Written by at least two authors (preferably from different institutions). Manuscripts must have a word count of not more than 4,000 words. The number of references used is no more than 10, with 80% of them coming from the last five years.
   c. Literature Review: Literature review is by invitation only and recommended by at least one editorial board member and written by at least two authors (preferably from different institutions). The number of words is not limited to at least 75 references, and 80% of them come from the last five years.
   d. Expert Opinion: Expert opinion is by invitation only and recommended by at least one editorial board member. The number of words is not limited to at least 20 references, and 80% of them come from the last five years. Experts must have published at least five manuscripts on the relevant theme, with an h-index (Scopus/Publons) of 5 and above being preferred.
8. Graphical abstracts are mandatory for submissions in the Journal of Molecular Docking and are submitted for the first time together with the entire manuscript. The size of the graphical abstract is not specified, but it must have a resolution of at least 300 dpi.
9. Figures are not submitted separately but are joined together with the submitted manuscript. Copyediting editors can adjust the position of figures in the manuscript depending on needs, and the authors must provide a clear identity for each figure. Ideally, the figures used have a minimum size of 500 × 800 pixels (height × width), with clear and sharp resolution so they can be seen at 100% magnification (at least 300 dpi for color and black-and-white figures). Symbols and data sets must be clear and easily distinguishable. For charts, avoid graphic plots that are too crowded. Figures should always be cited in text in consecutive numerical order. Figure parts should be denoted by lowercase letters (a, b, c, etc.). If you include figures that have already been published elsewhere, you must obtain permission from the copyright owner(s) for both the print and online format. In such cases, material from other sources should be used.
10. Tables should always be in editable text and not as images (don't copy and paste tables from other sources). Number tables consecutively by their appearance in the text and place any notes below the table body. The data presented in the table must not duplicate the results described elsewhere in the article. Avoid using vertical rules and shading in table cells. Tables should always be cited in text in consecutive numerical order.
11. The unit used is the International Units System (see https://www.britannica.com/science/International-System-of-Units).
12. Equations are numbered in parentheses and be numbered consecutively. All equation numbers must appear on the right-hand side of the equation and refer to within the text. Except, equations that only appear once and are not referred to in the next part of the text (e.g., only show formulas) are not numbered. Equations must be created using Microsoft Word's equation menu and not pasted figures.
13. Guideline for Online Submission: The author should first register as an Author Role and be offered as a Reviewer by the address http://journal.umpalangkaraya.ac.id/index.php/jmd/submission/wizard. A star-marked form must be entered; the author should fill out the form as detailed as possible. After all the form textbox has been filled in, the author clicks the "Register" button to proceed with the registration process. Therefore, the author is sent to an online author submission interface where the author should click on "Make a submission." In the Start New Submission section, click "'Make a new submission' to go to step one of the five-step submission processes." Five steps in the online submission process are as follows:
    a. Start: Select the appropriate section of the journal. Thus, the author must use a checkmark on the submission checklists. An author should type or copy-paste the Cover Letter in Comments for the Editor.
    b. Upload Submission: To upload a manuscript to this journal, click Browse on the Upload submission file item and choose the manuscript document file (.doc/.docx) to be submitted, then click the "Upload" button until the file has been uploaded. The cover letter and other supplementary files are also uploaded here.
    c. Enter Metadata: In this step, the metadata authors' details should be entered, including the marked corresponding author. Authors are strongly advised to complete the authors' identity, including adding the correct ORCiD. After that, the manuscript title and abstract must be uploaded by copying the text and pasting it in the textbox, including keywords. Other required metadata is languages ​​and references.
    d. Confirmation: In this step, the author should finally check the uploaded manuscript documents. To submit a manuscript to the Journal of Molecular Docking, click the Finish Submission button when the documents are valid. The corresponding author or principal contact will receive an acknowledgment by email. It will be able to view the submission progress through the editorial process by logging in to the journal's website address.
    e. Next Steps: This contains additional information for authors, such as whether the authors want to make other submissions or return to the author's dashboard. After this submission, the Authors who submit the manuscript will automatically receive an email confirmation. Authors can therefore track their submission status at any time by logging in to the online submission interface. Submission monitoring includes the status of the Manuscript Review and Editorial Process.