{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T07:20:23Z","timestamp":1782372023297,"version":"3.54.5"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,7]],"date-time":"2024-03-07T00:00:00Z","timestamp":1709769600000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200100"],"award-info":[{"award-number":["2021YFF1200100"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32101182"],"award-info":[{"award-number":["32101182"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32201175"],"award-info":[{"award-number":["32201175"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Science, Technology and Innovation Commission"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and\/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Our tool is publicly available at https:\/\/github.com\/BGI-SynBio\/PyMOL-PUB.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae139","type":"journal-article","created":{"date-parts":[[2024,3,7]],"date-time":"2024-03-07T06:04:12Z","timestamp":1709791452000},"source":"Crossref","is-referenced-by-count":19,"title":["Rapid generation of high-quality structure figures for publication with PyMOL-PUB"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-9972-2060","authenticated-orcid":false,"given":"Yuting","family":"Chen","sequence":"first","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"BGI Research , Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4507-0339","authenticated-orcid":false,"given":"Haoling","family":"Zhang","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3359-1030","authenticated-orcid":false,"given":"Wen","family":"Wang","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen 518083, China"},{"name":"BGI Research , Changzhou 213299, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3276-7295","authenticated-orcid":false,"given":"Yue","family":"Shen","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen 518083, China"},{"name":"BGI Research , Changzhou 213299, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7114-1124","authenticated-orcid":false,"given":"Zhi","family":"Ping","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen 518083, China"},{"name":"BGI Research , Changzhou 213299, China"},{"name":"School of Medicine, The Chinese University of Hong Kong , Shenzhen 518172, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,3,6]]},"reference":[{"key":"2024050808060830800_btae139-B1","volume-title":"Hands-On Continuous Integration and Delivery: Build and Release Quality Software at Scale with Jenkins, Travis CI, and CircleCI","author":"Belmont","year":"2018"},{"key":"2024050808060830800_btae139-B2","first-page":"82","article-title":"Pymol: an open-source molecular graphics tool","volume":"40","author":"DeLano","year":"2002","journal-title":"CCP4 Newsletter on Protein 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recognition of synaptic vesicle protein 2","volume":"14","author":"Liu","year":"2023","journal-title":"Nat Commun"},{"key":"2024050808060830800_btae139-B7","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.3390\/molecules25051030","article-title":"Protein x-ray crystallography and drug discovery","volume":"25","author":"Maveyraud","year":"2020","journal-title":"Molecules"},{"key":"2024050808060830800_btae139-B8","volume-title":"Python GUI Programming Cookbook: Develop Functional and Responsive User Interfaces with tkinter and PyQt5","author":"Meier","year":"2019"},{"key":"2024050808060830800_btae139-B9","doi-asserted-by":"crossref","first-page":"4587","DOI":"10.1063\/1.532988","article-title":"On the root mean square quantitative chirality and quantitative symmetry measures","volume":"40","author":"Petitjean","year":"1999","journal-title":"Journal of Mathematical 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