{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:34Z","timestamp":1740185134813,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,11]],"date-time":"2020-08-11T00:00:00Z","timestamp":1597104000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["SFB 815"],"award-info":[{"award-number":["SFB 815"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We provide a software to describe the topology of large protein complexes based mainly on cryo-EM data and stored as macromolecular Crystallographic Information Files (mmCIFs) in the PDB. The software extends the Protein Topology Graph Library and implements an efficient file parser to analyze mmCIFs. The extended Protein Topology Graph Library includes a graph-based representation of the topology of protein complexes on the supersecondary and quaternary structure level. The library holds topology graphs of 151\u00a0837 PDB files; 921 of them are large structures. The abstraction of protein structure complexes to undirected labeled graphs enables classification and comparison of large protein complexes on quaternary structure level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Online access at http:\/\/ptgl.uni-frankfurt.de. Source code in Java under GNU public license 2.0 at https:\/\/github.com\/MolBIFFM\/vplg.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa706","type":"journal-article","created":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T11:29:59Z","timestamp":1596194999000},"page":"1032-1034","source":"Crossref","is-referenced-by-count":5,"title":["PTGL: extension to graph-based topologies of cryo-EM data for large protein structures"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0536-9400","authenticated-orcid":false,"given":"Jan Niclas","family":"Wolf","sequence":"first","affiliation":[{"name":"Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main , 60325 Frankfurt am Main, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5652-8424","authenticated-orcid":false,"given":"Marcus","family":"Ke\u00dfler","sequence":"additional","affiliation":[{"name":"Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main , 60325 Frankfurt am Main, Germany"}]},{"given":"J\u00f6rg","family":"Ackermann","sequence":"additional","affiliation":[{"name":"Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main , 60325 Frankfurt am Main, Germany"}]},{"given":"Ina","family":"Koch","sequence":"additional","affiliation":[{"name":"Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main , 60325 Frankfurt am Main, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,8,11]]},"reference":[{"key":"2023051612175806700_btaa706-B1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023051612175806700_btaa706-B2","doi-asserted-by":"crossref","first-page":"D289","DOI":"10.1093\/nar\/gkw1098","article-title":"CATH: an expanded resource to predict protein function through structure and sequence","volume":"45","author":"Dawson","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023051612175806700_btaa706-B3","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.str.2005.01.008","article-title":"Large macromolecular complexes in the Protein Data Bank: a status report","volume":"13","author":"Dutta","year":"2005","journal-title":"Structure"},{"key":"2023051612175806700_btaa706-B4","doi-asserted-by":"crossref","first-page":"D304","DOI":"10.1093\/nar\/gkt1240","article-title":"SCOPe: structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures","volume":"42","author":"Fox","year":"2014","journal-title":"Nucleic Acids Res"},{"volume-title":"Technical report","year":"1997","author":"Himsolt","key":"2023051612175806700_btaa706-B19"},{"key":"2023051612175806700_btaa706-B5","doi-asserted-by":"crossref","first-page":"5326","DOI":"10.1093\/bioinformatics\/btz536","article-title":"Benchmarking fold detection by DaliLite v.5","volume":"35","author":"Holm","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051612175806700_btaa706-B6","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/S0022-5193(05)80253-X","article-title":"Knowledge-based prediction of protein structures","volume":"147","author":"Kaden","year":"1990","journal-title":"J. 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