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Submission Preparation Checklist

As part of the submission process, authors are required to check off their submission's compliance with all of the following items, and submissions may be returned to authors that do not adhere to these guidelines.
  • The submission has not been previously published, nor is it before another journal for consideration (or an explanation has been provided in Comments to the Editor).
  • The submission file is in OpenOffice, Microsoft Word, or RTF document file format.
  • Where available, URLs for the references have been provided.
  • The text is 1.08 spaced; uses an 11-point font; employs italics, rather than underlining (except with URL addresses); and all illustrations, figures, and tables are placed within the text at the appropriate points, rather than at the end.
  • The text adheres to the stylistic and bibliographic requirements outlined in the Author Guidelines.

Author Guidelines

  1. Writing is the result of research or review of critical analysis study in the field but not limited to Pharmacy, Chemistry, Physics, Bioinformatics, and other fields that utilize molecular docking methods which have never been published in other scientific publication media.
  2. Manuscripts that have been 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 (Title page) and HERE (Manuscript).
  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 clear, 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, as well as 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 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 is a summary of the article. The abstract is created in one paragraph and a maximum of 250 words 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 separated by a semicolon.
    d. Authors' contributions: contain 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: consists of at least three parts, namely an introduction to the topic, a summary of the state of the art, and a research gap including the research objectives. Citation is written in Vancouver style using letters in square brackets [1], [2,3], [4-6].
    f. Method: Hardware and Software: State the hardware system (Type, Brand, OS, CPU) along with 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, just 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 used is adopted from previous research, it does not need to be written in full and only mentions the references used.
    Assessment: The parameters used in assessing and ranking the test ligands of the docking results are clearly stated.
    g. Results and Discussion: The results and discussion are presented in the same chapter. Results should be presented in either tabular or graphical form. The discussion contains an emphasis on three things: Explanation of the results obtained, comparison with previous research, and prospects for further research in the future.
    h. Conclusion: contains a brief explanation that directly answers the research objectives. The conclusion should not contain citations or other things that are not related to the purpose of the research.
    i. Conflicts of interest: Contains information on possible conflicts of interest of authors. If not, 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 the source of funding from a research along with 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 the results of research that the authors upload independently both on the preprint server 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 minimum number of references is 20, with 80% from primary sources and published in the last five years. 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 contact the Editorial Office at lp2m@umpalangkaraya.ac.id or mohammadrizkifadhilpratama@gmail.com. The Cover letter outlines the basic 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. Determination of the type of manuscript is determined by the authors based on the content of each manuscript, editors only continue to type the manuscript that has been chosen by the authors. The general difference between original research articles and short communication lies in the length and depth of the content of the manuscript.
    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% of them 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 references 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. Written by at least two authors (preferably from different institutions). The number of words is not limited with 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 with 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. The position of figures in the manuscript can be adjusted by copyediting editors 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 that they can be seen at 100% magnification.
  10. Guideline for Online Submission: The author should first register as an Author Role and may be offered as a Reviewer by the address http:/journal.umpalangkaraya.ac.id/ index.php/jmd/submission/wizard. Where 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. The Author is therefore 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 checkmark on the submission checklists. An author should type or copy-paste the Covering 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 true. The corresponding author or principal contact will receive an acknowledgment by e-mail and will be able to view the progress of the submission through the editorial process by logging in to the journal's website address.
    e. Next Steps: 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 of the submission. Authors are therefore able to 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.

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