{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T02:52:20Z","timestamp":1772506340204,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,6,13]],"date-time":"2024-06-13T00:00:00Z","timestamp":1718236800000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Education and King Abdulaziz University, DSR, Jeddah, Saudi Arabia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Molecular dynamics (MD) is a computational experiment that is crucial for understanding the structure of biological macro and micro molecules, their folding, and the inter-molecular interactions. Accurate knowledge of these structural features is the cornerstone in drug development and elucidating macromolecules functions. The open-source GROMACS biomolecular MD simulation program is recognized as a reliable and frequently used simulation program for its precision. However, the user requires expertise, and scripting skills to carrying out MD simulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed an end-to-end interactive MD simulation application, MolDy for Gromacs. This front-end application provides a customizable user interface integrated with the Python and Perl-based logical backend connecting the Linux shell and Gromacs software. The tool performs analysis and provides the user with simulation trajectories and graphical representations of relevant biophysical parameters. The advantages of MolDy are (i) user-friendly, does not requiring the researcher to have prior knowledge of Linux; (ii) easy installation by a single command; (iii) freely available for academic research; (iv) can run with minimum configuration of operating systems; (v) has valid default prefilled parameters for beginners, and at the same time provides scope for modifications for expert users.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MolDy is available freely as compressed source code files with user manual for installation and operation on GitHub: https:\/\/github.com\/AIBResearchMolDy\/Moldyv01.git and on https:\/\/aibresearch.com\/innovations.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae313","type":"journal-article","created":{"date-parts":[[2024,6,13]],"date-time":"2024-06-13T10:26:23Z","timestamp":1718274383000},"source":"Crossref","is-referenced-by-count":6,"title":["MolDy: molecular dynamics simulation made easy"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-8896-9619","authenticated-orcid":false,"given":"Mohd Imran","family":"Khan","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India"}]},{"given":"Sheetal","family":"Pathania","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India"}]},{"given":"Mohammed W","family":"Al-Rabia","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdul Aziz University , Jeddah 21589, Saudi Arabia"},{"name":"Department of Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital , Jeddah 21589, Saudi Arabia"}]},{"given":"Abdul S","family":"Ethayathulla","sequence":"additional","affiliation":[{"name":"Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India"}]},{"given":"Mohammad Imran","family":"Khan","sequence":"additional","affiliation":[{"name":"Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia"}]},{"given":"Khaled S","family":"Allemailem","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4623-9557","authenticated-orcid":false,"given":"Mohd","family":"Azam","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia"}]},{"given":"Gururao","family":"Hariprasad","sequence":"additional","affiliation":[{"name":"Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India"}]},{"given":"Mohammad Azhar","family":"Imran","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. 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