{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T15:55:41Z","timestamp":1781366141776,"version":"3.54.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,4,30]],"date-time":"2022-04-30T00:00:00Z","timestamp":1651276800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018929","name":"de.NBI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100018929","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Federal Ministry of Education and Research","award":["031L0105"],"award-info":[{"award-number":["031L0105"]}]},{"name":"German Federal Ministry of Education and Research","award":["031L0172"],"award-info":[{"award-number":["031L0172"]}]},{"name":"German Federal Ministry of Education and Research","award":["031L0105"],"award-info":[{"award-number":["031L0105"]}]},{"name":"German Federal Ministry of Education and Research","award":["031B0405B"],"award-info":[{"award-number":["031B0405B"]}]},{"name":"Data Science in Hamburg"},{"name":"Helmholtz Graduate School"},{"DOI":"10.13039\/501100001656","name":"Helmholtz Association","doi-asserted-by":"publisher","award":["HIDSS-0002"],"award-info":[{"award-number":["HIDSS-0002"]}],"id":[{"id":"10.13039\/501100001656","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for Data and Computing in Natural Sciences"},{"name":"Authority for Science, Research and Equality of the Free and Hanseatic City of Hamburg","award":["LFF-HHX-03"],"award-info":[{"award-number":["LFF-HHX-03"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Upon the ever-increasing number of publicly available experimentally determined and predicted protein and nucleic acid structures, the demand for easy-to-use tools to investigate these structural models is higher than ever before. The ProteinsPlus web server (https:\/\/proteins.plus) comprises a growing collection of molecular modeling tools focusing on protein\u2013ligand interactions. It enables quick access to structural investigations ranging from structure analytics and search methods to molecular docking. It is by now well-established in the community and constantly extended. The server gives easy access not only to experts but also to students and occasional users from the field of life sciences. Here, we describe its recently added new features and tools, beyond them a novel method for on-the-fly molecular docking and a search method for single-residue substitutions in local regions of a protein structure throughout the whole Protein Data Bank. Finally, we provide a glimpse into new avenues for the annotation of AlphaFold structures which are directly accessible via a RESTful service on the ProteinsPlus web server.<\/jats:p>","DOI":"10.1093\/nar\/gkac305","type":"journal-article","created":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T19:22:57Z","timestamp":1650396177000},"page":"W611-W615","source":"Crossref","is-referenced-by-count":190,"title":["Proteins<i>Plus<\/i>: a comprehensive collection of web-based molecular modeling tools"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3248-8023","authenticated-orcid":false,"given":"Katrin","family":"Sch\u00f6ning-Stierand","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8171-0888","authenticated-orcid":false,"given":"Konrad","family":"Diedrich","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1428-0042","authenticated-orcid":false,"given":"Christiane","family":"Ehrt","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7051-8719","authenticated-orcid":false,"given":"Florian","family":"Flachsenberg","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8327-4936","authenticated-orcid":false,"given":"Joel","family":"Graef","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5343-7255","authenticated-orcid":false,"given":"Jochen","family":"Sieg","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4988-6183","authenticated-orcid":false,"given":"Patrick","family":"Penner","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8529-8376","authenticated-orcid":false,"given":"Martin","family":"Poppinga","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"},{"name":"Universit\u00e4t Hamburg, Department of Informatics, Vogt-K\u00f6lln-Stra\u00dfe 30 , 22527 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annett","family":"Ungeth\u00fcm","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, Center for Data and Computing in Natural Sciences (CDCS), Notkestra\u00dfe 11 , 22607 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9553-6531","authenticated-orcid":false,"given":"Matthias","family":"Rarey","sequence":"additional","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43 , 20146 Hamburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,4,30]]},"reference":[{"key":"2022070423570871500_B1","doi-asserted-by":"crossref","first-page":"W48","DOI":"10.1093\/nar\/gkaa235","article-title":"ProteinsPlus: interactive analysis of protein\u2013ligand binding interfaces","volume":"48","author":"Sch\u00f6ning-Stierand","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022070423570871500_B2","doi-asserted-by":"crossref","first-page":"W337","DOI":"10.1093\/nar\/gkx333","article-title":"Proteins plus: a web portal for structure analysis of macromolecules","volume":"45","author":"F\u00e4hrrolfes","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2022070423570871500_B3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank (www.rcsb.org)","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2022070423570871500_B4","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":"2022070423570871500_B5","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1021\/acs.jmedchem.1c01046","article-title":"Searching geometric patterns in protein binding sites and their application to data mining in protein kinase structures","volume":"65","author":"Graef","year":"2022","journal-title":"J. Med. Chem."},{"key":"2022070423570871500_B6","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1093\/bioinformatics\/btaa693","article-title":"GeoMine: interactive pattern mining of protein\u2013ligand interfaces in the protein data bank","volume":"37","author":"Diedrich","year":"2021","journal-title":"Bioinformatics"},{"key":"2022070423570871500_B7","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1093\/bioinformatics\/bts310","article-title":"DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment","volume":"28","author":"Volkamer","year":"2012","journal-title":"Bioinformatics"},{"key":"2022070423570871500_B8","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1758-2946-6-12","article-title":"Protoss: a holistic approach to predict tautomers and protonation states in protein\u2013ligand complexes","volume":"6","author":"Bietz","year":"2014","journal-title":"J. Cheminform."},{"key":"2022070423570871500_B9","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1758-2946-1-13","article-title":"Fast automated placement of polar hydrogen atoms in protein\u2013ligand complexes","volume":"1","author":"Lippert","year":"2009","journal-title":"J. Cheminform."},{"key":"2022070423570871500_B10","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1021\/acs.jcim.6b00069","article-title":"UNICON: a powerful and Easy-to-Use compound library converter","volume":"56","author":"Sommer","year":"2016","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B11","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1021\/acs.jcim.8b00704","article-title":"Conformator: a novel method for the generation of conformer ensembles","volume":"59","author":"Friedrich","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B12","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1021\/ci9000212","article-title":"Beyond the virtual screening paradigm: structure-based searching for new lead compounds","volume":"49","author":"Schlosser","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B13","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1007\/s10822-014-9769-4","article-title":"An integrated approach to knowledge-driven structure-based virtual screening","volume":"28","author":"Henzler","year":"2014","journal-title":"J. Comput. Aided. Mol. Des."},{"key":"2022070423570871500_B14","doi-asserted-by":"crossref","first-page":"6502","DOI":"10.1021\/acs.jcim.0c01095","article-title":"A consistent scheme for gradient-based optimization of protein\u2013ligand poses","volume":"60","author":"Flachsenberg","year":"2020","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B15","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1002\/jcc.26522","article-title":"LSLOpt: an open-source implementation of the step-length controlled LSL-BFGS algorithm","volume":"42","author":"Flachsenberg","year":"2021","journal-title":"J. Comput. Chem."},{"key":"2022070423570871500_B16","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1021\/ci100241y","article-title":"Analyzing the topology of active sites: on the prediction of pockets and subpockets","volume":"50","author":"Volkamer","year":"2010","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B17","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1021\/acs.jcim.5b00210","article-title":"ASCONA: rapid detection and alignment of protein binding site conformations","volume":"55","author":"Bietz","year":"2015","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B18","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1021\/acs.jcim.5b00588","article-title":"SIENA: efficient compilation of selective protein binding site ensembles","volume":"56","author":"Bietz","year":"2016","journal-title":"J. Chem. Inf. Model."},{"key":"2022070423570871500_B19","doi-asserted-by":"crossref","first-page":"e54046","DOI":"10.15252\/embr.202154046","article-title":"AI revolutions in biology","volume":"22","author":"Perrakis","year":"2021","journal-title":"EMBO Rep."},{"key":"2022070423570871500_B20","doi-asserted-by":"crossref","DOI":"10.1101\/2021.11.26.470110","article-title":"AlphaFill: enriching the alphafold models with ligands and co-factors","author":"Hekkelman","year":"2021"},{"key":"2022070423570871500_B21","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1093\/bioinformatics\/btl150","article-title":"Molecular complexes at a glance: automated generation of two-dimensional complex diagrams","volume":"22","author":"Stierand","year":"2006","journal-title":"Bioinformatics"},{"key":"2022070423570871500_B22","doi-asserted-by":"crossref","first-page":"4827","DOI":"10.1021\/acs.jcim.1c01114","article-title":"AlphaFold 2: why it works and its implications for understanding the relationships of protein sequence, structure, and function","volume":"61","author":"Skolnick","year":"2021","journal-title":"J. Chem. Inf. Model."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W611\/44376012\/gkac305.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W611\/44376012\/gkac305.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T23:58:06Z","timestamp":1656979086000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W611\/6576358"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,30]]},"references-count":22,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2022,4,30]]},"published-print":{"date-parts":[[2022,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac305","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,7,5]]},"published":{"date-parts":[[2022,4,30]]}}}