{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T11:38:33Z","timestamp":1774525113964,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T00:00:00Z","timestamp":1676419200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Natural Science Foundation of Xianning","award":["2022ZRKX066"],"award-info":[{"award-number":["2022ZRKX066"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2662022XXYJ010"],"award-info":[{"award-number":["2662022XXYJ010"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Research Incubator Program of HBUST","award":["2022-24GP02"],"award-info":[{"award-number":["2022-24GP02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The preprocessed initial files that feed the molecular dynamics (MD) simulation packages dramatically influence the outcome of the simulations. However, the popular MD simulation packages depend, to a great extent, on the user\u2019s experience in the preparation of MD simulation systems. In this work, we present an easy-to-use tool called MDBuilder, a PyMOL plugin that assists researchers in building the starting structures for multiple popular MD simulation packages. MDBuilder is not only designed to assist MD beginners to overcome the steep learning curve by providing a menu-oriented, point-and-click user graphic interface (GUI), but also to provide an alternative way to prepare the input files for some highly scalable CHARMM force field-based MD simulation packages. The platform-independent GUI is implemented as a PyMOL plugin using the Python language, and it has been tested on Windows and Linux platforms. The source code and documentation of MDBuilder can be downloaded freely from https:\/\/github.com\/HuiLiuCode\/MDBuilder under the GNU General Public License.<\/jats:p>","DOI":"10.1093\/bib\/bbad057","type":"journal-article","created":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T16:54:27Z","timestamp":1676480067000},"source":"Crossref","is-referenced-by-count":22,"title":["MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1267-2475","authenticated-orcid":false,"given":"Hui","family":"Liu","sequence":"first","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics , College of Informatics, , Wuhan, Hubei 430070 , China"},{"name":"Huazhong Agricultural University , College of Informatics, , Wuhan, Hubei 430070 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ye","family":"Jin","sequence":"additional","affiliation":[{"name":"Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou, Jiangsu 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0659-0457","authenticated-orcid":false,"given":"Hanjing","family":"Ding","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Hubei University of Science and Technology , Xianning, Hubei 437100 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,2,15]]},"reference":[{"key":"2023032004465242700_","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/nsb0902-646","article-title":"Molecular dynamics simulations of biomolecules","volume":"9","author":"Karplus","year":"2002","journal-title":"Nat Struct 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