{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:04Z","timestamp":1753875784218,"version":"3.41.2"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T00:00:00Z","timestamp":1702339200000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation funding","award":["BB\/W017970\/1","DBI-2129634"],"award-info":[{"award-number":["BB\/W017970\/1","DBI-2129634"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218303\/Z\/19\/Z"],"award-info":[{"award-number":["218303\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Molecular Biology Laboratory\u2014European Bioinformatics Institute"},{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["22-30571M"],"award-info":[{"award-number":["22-30571M"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types, and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PDBImages is available as an npm package from https:\/\/www.npmjs.com\/package\/pdb-images. The source code is available from https:\/\/github.com\/PDBeurope\/pdb-images.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad744","type":"journal-article","created":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T22:51:10Z","timestamp":1702421470000},"source":"Crossref","is-referenced-by-count":0,"title":["PDBImages: a command-line tool for automated macromolecular structure visualization"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0455-2235","authenticated-orcid":false,"given":"Adam","family":"Midlik","sequence":"first","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6861-7627","authenticated-orcid":false,"given":"Sreenath","family":"Nair","sequence":"additional","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4838-443X","authenticated-orcid":false,"given":"Stephen","family":"Anyango","sequence":"additional","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9043-7665","authenticated-orcid":false,"given":"Mandar","family":"Deshpande","sequence":"additional","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0682-3089","authenticated-orcid":false,"given":"David","family":"Sehnal","sequence":"additional","affiliation":[{"name":"Biological Data Management and Analysis Core Facility, Centre for Structural Biology, CEITEC\u2014Central European Institute of Technology, Masaryk University , Brno 62500, Czech Republic"},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno 62500, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3687-0839","authenticated-orcid":false,"given":"Mihaly","family":"Varadi","sequence":"additional","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8439-5964","authenticated-orcid":false,"given":"Sameer","family":"Velankar","sequence":"additional","affiliation":[{"name":"Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,12,12]]},"reference":[{"key":"2023122305563635100_btad744-B1","doi-asserted-by":"crossref","first-page":"D376","DOI":"10.1093\/nar\/gkz1064","article-title":"The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures","volume":"48","author":"Andreeva","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B2","first-page":"D335","article-title":"PDBe: improved findability of macromolecular structure data in the PDB","volume":"48","author":"Armstrong","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B3","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022","volume":"50","author":"Cunningham","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B4","doi-asserted-by":"crossref","first-page":"D482","DOI":"10.1093\/nar\/gky1114","article-title":"SIFTS: updated structure integration with function, taxonomy and sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins","volume":"47","author":"Dana","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B5","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/j.sbi.2007.06.008","article-title":"Visualisation software for molecular assemblies","volume":"17","author":"Goddard","year":"2007","journal-title":"Curr Opin Struct Biol"},{"key":"2023122305563635100_btad744-B6","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1002\/ijch.201300024","article-title":"JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia","volume":"53","author":"Hanson","year":"2013","journal-title":"Isr J Chem"},{"first-page":"55","year":"2014","author":"Heinrich","key":"2023122305563635100_btad744-B7"},{"key":"2023122305563635100_btad744-B8","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023122305563635100_btad744-B9","doi-asserted-by":"crossref","first-page":"D192","DOI":"10.1093\/nar\/gkaa1047","article-title":"Rfam 14: expanded coverage of metagenomic, viral and microRNA families","volume":"49","author":"Kalvari","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B10","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1111\/cgf.13072","article-title":"Visualization of biomolecular structures: state of the art revisited","volume":"36","author":"Kozl\u00edkov\u00e1","year":"2017","journal-title":"Comput Graph Forum"},{"key":"2023122305563635100_btad744-B11","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B12","doi-asserted-by":"crossref","first-page":"669186","DOI":"10.3389\/fbinf.2021.669186","article-title":"Grand challenges in bioinformatics data visualization","volume":"1","author":"O'Donoghue","year":"2021","journal-title":"Front Bioinform"},{"key":"2023122305563635100_btad744-B13","doi-asserted-by":"crossref","first-page":"S42","DOI":"10.1038\/nmeth.1427","article-title":"Visualization of macromolecular structures","volume":"7","author":"O'Donoghue","year":"2010","journal-title":"Nat Methods"},{"key":"2023122305563635100_btad744-B14","doi-asserted-by":"crossref","first-page":"3997","DOI":"10.1016\/j.jmb.2018.07.009","article-title":"Perspectives on structural molecular biology visualization: from past to present","volume":"430","author":"Olson","year":"2018","journal-title":"J Mol Biol"},{"key":"2023122305563635100_btad744-B15","doi-asserted-by":"crossref","first-page":"D418","DOI":"10.1093\/nar\/gkac993","article-title":"InterPro in 2022","volume":"51","author":"Paysan-Lafosse","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B16","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: structure visualization for researchers, educators, and developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Sci"},{"author":"Schr\u00f6dinger, LLC","key":"2023122305563635100_btad744-B17"},{"key":"2023122305563635100_btad744-B18","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B19","doi-asserted-by":"crossref","first-page":"D266","DOI":"10.1093\/nar\/gkaa1079","article-title":"CATH: increased structural coverage of functional space","volume":"49","author":"Sillitoe","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B20","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"The UniProt Consortium","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2023122305563635100_btad744-B21","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2021","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad744\/54346070\/btad744.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/12\/btad744\/54770619\/btad744.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/12\/btad744\/54770619\/btad744.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,23]],"date-time":"2023-12-23T05:56:58Z","timestamp":1703311018000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad744\/7470737"}},"subtitle":[],"editor":[{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,12,1]]},"references-count":21,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2023,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad744","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,12,1]]},"published":{"date-parts":[[2023,12,1]]},"article-number":"btad744"}}