{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T11:39:08Z","timestamp":1780573148470,"version":"3.54.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,4,16]],"date-time":"2020-04-16T00:00:00Z","timestamp":1586995200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"de.NBI"},{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"publisher","award":["031L0105"],"award-info":[{"award-number":["031L0105"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task. The ProteinsPlus web service (https:\/\/proteins.plus) offers a broad range of tools addressing these challenges. The web interface to the tool collection focusing on protein\u2013ligand interactions has been geared towards easy and intuitive access to a large variety of functionality for life scientists. Since our last publication, the ProteinsPlus web service has been extended by additional services as well as it has undergone substantial infrastructural improvements. A keyword search functionality was added on the start page of ProteinsPlus enabling users to work on structures without knowing their PDB code. The tool collection has been augmented by three tools: StructureProfiler validates ligands and active sites using selection criteria of well-established protein\u2013ligand benchmark data sets, WarPP places water molecules in the ligand binding sites of a protein, and METALizer calculates, predicts and scores coordination geometries of metal ions based on surrounding complex atoms. Additionally, all tools provided by ProteinsPlus are available through a REST service enabling the automated integration in structure processing and modeling pipelines.<\/jats:p>","DOI":"10.1093\/nar\/gkaa235","type":"journal-article","created":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T11:10:59Z","timestamp":1586862659000},"page":"W48-W53","source":"Crossref","is-referenced-by-count":229,"title":["ProteinsPlus: interactive analysis of protein\u2013ligand binding interfaces"],"prefix":"10.1093","volume":"48","author":[{"given":"Katrin","family":"Sch\u00f6ning-Stierand","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konrad","family":"Diedrich","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rainer","family":"F\u00e4hrrolfes","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Flachsenberg","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8519-5780","authenticated-orcid":false,"given":"Agnes","family":"Meyder","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Nittinger","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruben","family":"Steinegger","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9553-6531","authenticated-orcid":false,"given":"Matthias","family":"Rarey","sequence":"first","affiliation":[{"name":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,4,16]]},"reference":[{"key":"2020062614040391300_B1","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":"2020062614040391300_B2","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1002\/pro.3730","article-title":"RCSB Protein Data Bank: enabling biomedical research and drug discovery","volume":"29","author":"Goodsell","year":"2020","journal-title":"Protein Sci."},{"key":"2020062614040391300_B3","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1016\/j.drudis.2012.06.011","article-title":"Essential considerations for using protein\u2013ligand structures in drug discovery","volume":"17","author":"Warren","year":"2012","journal-title":"Drug Discov. Today"},{"key":"2020062614040391300_B4","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1021\/jm061277y","article-title":"Diverse, high-quality test set for the validation of protein\u2013ligand docking performance","volume":"50","author":"Hartshorn","year":"2007","journal-title":"J. Med. Chem."},{"key":"2020062614040391300_B5","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkz424","article-title":"PrankWeb: a web server for ligand binding site prediction and visualization","volume":"47","author":"Jendele","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B6","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkv315","article-title":"PLIP: fully automated protein\u2013ligand interaction profiler","volume":"43","author":"Salentin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B7","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.jmb.2016.12.004","article-title":"Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures","volume":"429","author":"Jubb","year":"2017","journal-title":"J. Mol. Biol."},{"key":"2020062614040391300_B8","doi-asserted-by":"crossref","first-page":"W331","DOI":"10.1093\/nar\/gkz368","article-title":"Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein\u2013protein interactions","volume":"47","author":"Roy","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B9","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1002\/jcc.21303","article-title":"Crystal contacts as nature's docking solutions","volume":"31","author":"Evgeny","year":"2010","journal-title":"J. Comput. Chem."},{"key":"2020062614040391300_B10","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1007\/s00775-014-1128-3","article-title":"MetalS3, a database-mining tool for the identification of structurally similar metal sites","volume":"19","author":"Valasatava","year":"2014","journal-title":"J. Biol. Inorg. Chem."},{"key":"2020062614040391300_B11","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1107\/S2059798317001061","article-title":"CheckMyMetal: a macromolecular metal-binding validation tool","volume":"73","author":"Zheng","year":"2017","journal-title":"Acta Crystallogr. Sect. D Struct. Biol."},{"key":"2020062614040391300_B12","doi-asserted-by":"crossref","first-page":"D459","DOI":"10.1093\/nar\/gkx989","article-title":"MetalPDB in 2018: A database of metal sites in biological macromolecular structures","volume":"46","author":"Putignano","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B13","doi-asserted-by":"crossref","first-page":"D520","DOI":"10.1093\/nar\/gky949","article-title":"Protein Data Bank: the single global archive for 3D macromolecular structure data","volume":"47","author":"Burley","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B14","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gkz853","article-title":"PDBe-KB: a community-driven resource for structural and functional annotations","volume":"48","author":"PDBe-KB consortium","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B15","doi-asserted-by":"crossref","first-page":"D464","DOI":"10.1093\/nar\/gky1004","article-title":"RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy","volume":"47","author":"Burley","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B16","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":"2020062614040391300_B17","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.jmgm.2016.07.008","article-title":"Open source molecular modeling","volume":"69","author":"Pirhadi","year":"2016","journal-title":"J. Mol. Graph. Model."},{"key":"2020062614040391300_B18","doi-asserted-by":"crossref","first-page":"2437","DOI":"10.1021\/acs.jcim.7b00391","article-title":"Estimating electron density support for individual atoms and molecular fragments in X-ray structures","volume":"57","author":"Meyder","year":"2017","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B19","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1093\/bioinformatics\/bty692","article-title":"StructureProfiler: an all-in-one tool for 3D protein structure profiling","volume":"35","author":"Meyder","year":"2019","journal-title":"Bioinformatics"},{"key":"2020062614040391300_B20","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":"2020062614040391300_B21","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1021\/acs.jcim.8b00271","article-title":"Placement of water molecules in protein structures: from large-scale evaluations to single-case examples","volume":"58","author":"Nittinger","year":"2018","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B22","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":"2020062614040391300_B23","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":"2020062614040391300_B24","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1021\/ci200454v","article-title":"Combining global and local measures for structure-based druggability predictions","volume":"52","author":"Volkamer","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B25","doi-asserted-by":"crossref","first-page":"3755","DOI":"10.1093\/bioinformatics\/bty419","article-title":"NGL viewer: web-based molecular graphics for large complexes","volume":"34","author":"Rose","year":"2018","journal-title":"Bioinformatics"},{"key":"2020062614040391300_B26","doi-asserted-by":"crossref","first-page":"W576","DOI":"10.1093\/nar\/gkv402","article-title":"NGL Viewer: a web application for molecular visualization","volume":"43","author":"Rose","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B27","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1002\/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8","article-title":"Evaluation of the FlexX incremental construction algorithm for protein- ligand docking","volume":"37","author":"Kramer","year":"1999","journal-title":"Proteins Struct. Funct. Genet."},{"key":"2020062614040391300_B28","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1006\/jmbi.1996.0477","article-title":"A fast flexible docking method using an incremental construction algorithm","volume":"261","author":"Rarey","year":"1996","journal-title":"J. Mol. Biol."},{"key":"2020062614040391300_B29","doi-asserted-by":"crossref","first-page":"W337","DOI":"10.1093\/nar\/gkx333","article-title":"ProteinsPlus: a web portal for structure analysis of macromolecules","volume":"45","author":"F\u00e4hrrolfes","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B30","doi-asserted-by":"crossref","first-page":"4245","DOI":"10.1021\/acs.jmedchem.7b00101","article-title":"Large-scale analysis of hydrogen bond interaction patterns in protein-ligand interfaces","volume":"60","author":"Nittinger","year":"2017","journal-title":"J. Med. Chem."},{"key":"2020062614040391300_B31","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1021\/acs.jcim.7b00291","article-title":"NAOMInova: interactive geometric analysis of noncovalent interactions in macromolecular structures","volume":"57","author":"Inhester","year":"2017","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B32","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1002\/prot.21818","article-title":"Modeling of metal interaction geometries for protein\u2013ligand docking","volume":"71","author":"Seebeck","year":"2008","journal-title":"Proteins Struct. Funct. Genet."},{"key":"2020062614040391300_B33","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/bts246","article-title":"FindGeo: a tool for determining metal coordination geometry","volume":"28","author":"Andreini","year":"2012","journal-title":"Bioinformatics"},{"key":"2020062614040391300_B34","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF chimera - a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2020062614040391300_B35","doi-asserted-by":"crossref","first-page":"D542","DOI":"10.1093\/nar\/gky1048","article-title":"BRENDA in 2019: a European ELIXIR core data resource","volume":"47","author":"Jeske","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B36","doi-asserted-by":"crossref","first-page":"D930","DOI":"10.1093\/nar\/gky1075","article-title":"ChEMBL: towards direct deposition of bioassay data","volume":"47","author":"Mendez","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040391300_B37","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S2052252514009324","article-title":"The PDB-REDO server for macromolecular structure model optimization","volume":"1","author":"Joosten","year":"2014","journal-title":"IUCrJ"},{"key":"2020062614040391300_B38","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1021\/acs.jcim.6b00561","article-title":"Index-based searching of interaction patterns in large collections of protein-ligand interfaces","volume":"57","author":"Inhester","year":"2017","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B39","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1021\/ci500130e","article-title":"Facing the challenges of structure-based target prediction by inverse virtual screening","volume":"54","author":"Schomburg","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B40","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1021\/ci300469h","article-title":"Fast protein binding site comparison via an index-based screening technology","volume":"53","author":"Von\u00a0Behren","year":"2013","journal-title":"J. Chem. Inf. Model."},{"key":"2020062614040391300_B41","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1110\/ps.50601","article-title":"High-resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector","volume":"10","author":"Safo","year":"2001","journal-title":"Protein Sci."},{"key":"2020062614040391300_B42","doi-asserted-by":"crossref","first-page":"2749","DOI":"10.1073\/pnas.93.7.2749","article-title":"Batimastat, a potent matrix metalloproteinase inhibitor, exhibits an unexpected mode of binding","volume":"93","author":"Botos","year":"1996","journal-title":"Proc. Natl. Acad. Sci. U.S.A."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W48\/33433349\/gkaa235.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W48\/33433349\/gkaa235.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,27]],"date-time":"2020-06-27T06:22:55Z","timestamp":1593238975000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/W1\/W48\/5820880"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,16]]},"references-count":42,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2020,4,16]]},"published-print":{"date-parts":[[2020,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa235","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7,2]]},"published":{"date-parts":[[2020,4,16]]}}}