{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:07:24Z","timestamp":1775606844106,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,4]],"date-time":"2024-01-04T00:00:00Z","timestamp":1704326400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Since its establishment in 2013, BioLiP has become one of the widely used resources for protein\u2013ligand interactions. Nevertheless, several known issues occurred with it over the past decade. For example, the protein\u2013ligand interactions are represented in the form of single chain-based tertiary structures, which may be inappropriate as many interactions involve multiple protein chains (known as quaternary structures). We sought to address these issues, resulting in Q-BioLiP, a comprehensive resource for quaternary structure-based protein\u2013ligand interactions. The major features of Q-BioLiP include: (1) representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures; (2) pairing DNA\/RNA chains properly rather than separation; (3) providing both experimental and predicted binding affinities; (4) retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands\u2019 biological relevance; and (5) developing a new quaternary structure-based algorithm for the modelling of protein\u2013ligand complex structure. With these new features, Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions, including protein\u2013small molecule interaction, protein\u2013metal ion interaction, protein\u2013peptide interaction, protein\u2013protein interaction, protein\u2013DNA\/RNA interaction, and RNA\u2013small molecule interaction. Q-BioLiP is freely available at https:\/\/yanglab.qd.sdu.edu.cn\/Q-BioLiP\/.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae001","type":"journal-article","created":{"date-parts":[[2024,1,4]],"date-time":"2024-01-04T13:02:28Z","timestamp":1704373348000},"source":"Crossref","is-referenced-by-count":19,"title":["Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein\u2013ligand Interactions"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2361-8589","authenticated-orcid":false,"given":"Hong","family":"Wei","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences, Nankai University , Tianjin 300071, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8603-8250","authenticated-orcid":false,"given":"Wenkai","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences, Nankai University , Tianjin 300071, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0303-6693","authenticated-orcid":false,"given":"Zhenling","family":"Peng","sequence":"additional","affiliation":[{"name":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University , Qingdao 266237, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2912-7737","authenticated-orcid":false,"given":"Jianyi","family":"Yang","sequence":"additional","affiliation":[{"name":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University , Qingdao 266237, China"}]}],"member":"286","published-online":{"date-parts":[[2024,1,4]]},"reference":[{"key":"2024070607341496900_qzae001-B1","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkt1127","article-title":"FireDB: a compendium of biological and pharmacologically relevant ligands","volume":"42","author":"Maietta","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B2","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkm911","article-title":"Binding MOAD, a high-quality protein\u2013ligand database","volume":"36","author":"Benson","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B3","doi-asserted-by":"crossref","first-page":"4111","DOI":"10.1021\/jm048957q","article-title":"The PDBbind database:\u2009 methodologies and updates","volume":"48","author":"Wang","year":"2005","journal-title":"J Med Chem"},{"key":"2024070607341496900_qzae001-B4","doi-asserted-by":"crossref","first-page":"D1045","DOI":"10.1093\/nar\/gkv1072","article-title":"BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology","volume":"44","author":"Gilson","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B5","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1021\/acs.accounts.6b00491","article-title":"Forging the basis for developing protein\u2013ligand interaction scoring functions","volume":"50","author":"Liu","year":"2017","journal-title":"Acc Chem Res"},{"key":"2024070607341496900_qzae001-B6","doi-asserted-by":"crossref","first-page":"W438","DOI":"10.1093\/nar\/gky439","article-title":"COACH-D: improved protein\u2013ligand binding sites prediction with refined ligand-binding poses through molecular docking","volume":"46","author":"Wu","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B7","doi-asserted-by":"crossref","first-page":"2588","DOI":"10.1093\/bioinformatics\/btt447","article-title":"Protein\u2013ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment","volume":"29","author":"Yang","year":"2013","journal-title":"Bioinformatics"},{"key":"2024070607341496900_qzae001-B8","doi-asserted-by":"crossref","first-page":"D403","DOI":"10.1093\/nar\/gkac873","article-title":"HProteome-BSite: predicted binding sites and ligands in human 3D proteome","volume":"51","author":"Sim","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B9","doi-asserted-by":"crossref","first-page":"13685","DOI":"10.1073\/pnas.1705381114","article-title":"Structure-based prediction of ligand\u2013protein interactions on a genome-wide scale","volume":"114","author":"Hwang","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024070607341496900_qzae001-B10","doi-asserted-by":"crossref","first-page":"W13","DOI":"10.1093\/nar\/gkac250","article-title":"3DLigandSite: structure-based prediction of protein\u2013ligand binding sites","volume":"50","author":"McGreig","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B11","doi-asserted-by":"crossref","first-page":"W274","DOI":"10.1093\/nar\/gkad297","article-title":"Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers","volume":"51","author":"McGuffin","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B12","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1021\/acs.jcim.8b00545","article-title":"Comparative assessment of scoring functions: the CASF-2016 update","volume":"59","author":"Su","year":"2019","journal-title":"J Chem Inf Model"},{"key":"2024070607341496900_qzae001-B13","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1021\/acs.jcim.7b00049","article-title":"Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein\u2013ligand interactions","volume":"57","author":"Li","year":"2017","journal-title":"J Chem Inf Model"},{"key":"2024070607341496900_qzae001-B14","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1002\/jcc.20505","article-title":"An iterative knowledge-based scoring function to predict protein\u2013ligand interactions: II. validation of the scoring function","volume":"27","author":"Huang","year":"2006","journal-title":"J Comput Chem"},{"key":"2024070607341496900_qzae001-B15","doi-asserted-by":"crossref","first-page":"W159","DOI":"10.1093\/nar\/gkac394","article-title":"CB-Dock2: improved protein\u2013ligand blind docking by integrating cavity detection, docking and homologous template fitting","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B16","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J Comput Chem"},{"key":"2024070607341496900_qzae001-B17","doi-asserted-by":"crossref","first-page":"D1096","DOI":"10.1093\/nar\/gks966","article-title":"BioLiP: a semi-manually curated database for biologically relevant ligand\u2013protein interactions","volume":"41","author":"Yang","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B18","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1109\/TCBB.2020.3002776","article-title":"On monomeric and multimeric structures-based protein\u2013ligand interactions","volume":"19","author":"Dai","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2024070607341496900_qzae001-B19","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/S0076-6879(97)77032-0","article-title":"Macromolecular Crystallographic Information File","volume":"277","author":"Bourne","year":"1997","journal-title":"Methods Enzymol"},{"key":"2024070607341496900_qzae001-B20","doi-asserted-by":"crossref","first-page":"D392","DOI":"10.1093\/nar\/gkq1021","article-title":"The RCSB Protein Data Bank: redesigned web site and web services","volume":"39","author":"Rose","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B21","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1002\/prot.23174","article-title":"Assessment of ligand-binding residue predictions in CASP9","volume":"79","author":"Schmidt","year":"2011","journal-title":"Proteins"},{"key":"2024070607341496900_qzae001-B22","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1023\/A:1016357811882","article-title":"Further development and validation of empirical scoring functions for structure-based binding affinity prediction","volume":"16","author":"Wang","year":"2002","journal-title":"J Comput Aided Mol Des"},{"key":"2024070607341496900_qzae001-B23","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1002\/pro.3295","article-title":"Dockground: a comprehensive data resource for modeling of protein complexes","volume":"27","author":"Kundrotas","year":"2018","journal-title":"Protein Sci"},{"key":"2024070607341496900_qzae001-B24","doi-asserted-by":"crossref","first-page":"189","DOI":"10.12688\/f1000research.7931.1","article-title":"FreeSASA: an open source C library for solvent accessible surface area calculations","volume":"5","author":"Mitternacht","year":"2016","journal-title":"F1000Res"},{"key":"2024070607341496900_qzae001-B25","first-page":"e142","article-title":"DSSR: an integrated software tool for dissecting the spatial structure of RNA","volume":"43","author":"Lu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B26","doi-asserted-by":"crossref","first-page":"3260","DOI":"10.1093\/bioinformatics\/btw396","article-title":"Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals","volume":"32","author":"Hu","year":"2016","journal-title":"Bioinformatics"},{"key":"2024070607341496900_qzae001-B27","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1021\/acs.jcim.8b00019","article-title":"Improving sequence-based prediction of protein\u2013peptide binding residues by introducing intrinsic disorder and a consensus method","volume":"58","author":"Zhao","year":"2018","journal-title":"J Chem Inf Model"},{"key":"2024070607341496900_qzae001-B28","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1038\/s42256-023-00741-2","article-title":"Protein\u2013protein contact prediction by geometric triangle-aware protein language models","volume":"5","author":"Lin","year":"2023","journal-title":"Nat Mach Intell"},{"key":"2024070607341496900_qzae001-B29","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1093\/bioinformatics\/bty756","article-title":"Improving the prediction of protein\u2013nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods","volume":"35","author":"Su","year":"2019","journal-title":"Bioinformatics"},{"key":"2024070607341496900_qzae001-B30","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1093\/bioinformatics\/btaa1092","article-title":"Recognition of small molecule\u2013RNA binding sites using RNA sequence and structure","volume":"37","author":"Su","year":"2021","journal-title":"Bioinformatics"},{"key":"2024070607341496900_qzae001-B31","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/s41587-023-01773-0","article-title":"Fast and accurate protein structure search with Foldseek","volume":"42","author":"Van Kempen","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2024070607341496900_qzae001-B32","doi-asserted-by":"crossref","first-page":"D1214","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: improved services and an expanding collection of metabolites","volume":"44","author":"Hastings","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B33","doi-asserted-by":"crossref","first-page":"D1388","DOI":"10.1093\/nar\/gkaa971","article-title":"PubChem in 2021: new data content and improved web interfaces","volume":"49","author":"Kim","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024070607341496900_qzae001-B34","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2024070607341496900_qzae001-B35","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","article-title":"3Dmol.js: molecular visualization with WebGL","volume":"31","author":"Rego","year":"2015","journal-title":"Bioinformatics"},{"key":"2024070607341496900_qzae001-B36","article-title":"BioLiP2: an updated structure database for biologically relevant ligand\u2013protein interactions","volume":"52","author":"Zhang","year":"2024","journal-title":"Nucleic Acids Res"}],"container-title":["Genomics, Proteomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gpb\/advance-article-pdf\/doi\/10.1093\/gpbjnl\/qzae001\/55024557\/qzae001.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/22\/1\/qzae001\/58457634\/qzae001.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/22\/1\/qzae001\/58457634\/qzae001.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T03:34:39Z","timestamp":1720236879000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/doi\/10.1093\/gpbjnl\/qzae001\/7510854"}},"subtitle":[],"editor":[{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,1,4]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,5,9]]}},"URL":"https:\/\/doi.org\/10.1093\/gpbjnl\/qzae001","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.06.23.546351","asserted-by":"object"}]},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,2]]},"published":{"date-parts":[[2024,1,4]]},"article-number":"qzae001"}}