{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,19]],"date-time":"2026-07-19T08:08:47Z","timestamp":1784448527131,"version":"3.55.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2024,9,30]],"date-time":"2024-09-30T00:00:00Z","timestamp":1727654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wallenberg AI, Autonomous System and Software Program"},{"DOI":"10.13039\/501100004063","name":"Knut and Alice Wallenberg Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>It is important to assess the quality of modeled biomolecules to benchmark and assess the performance of different prediction methods. DockQ has emerged as the standard tool for assessing the quality of protein interfaces in model structures against given references. However, as predictions of large multimers with multiple chains become more common, DockQ needs to be updated with more functionality for robustness and speed. Moreover, as the field progresses and more methods are released to predict interactions between proteins and other types of molecules, such as nucleic acids and small molecules, it becomes necessary to have a tool that can assess all types of interactions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present a complete reimplementation of DockQ in pure Python. The updated version of DockQ is more portable, faster and introduces novel functionalities, such as automatic DockQ calculations for multiple interfaces and automatic chain mapping with multi-threading. These enhancements are designed to facilitate comparative analyses of protein complexes, particularly large multi-chain complexes. Furthermore, DockQ is now also able to score interfaces between proteins, nucleic acids, and small molecules.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>DockQ v2 is available online at: https:\/\/wallnerlab.org\/DockQ.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae586","type":"journal-article","created":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T07:21:22Z","timestamp":1727421682000},"source":"Crossref","is-referenced-by-count":90,"title":["DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7868-034X","authenticated-orcid":false,"given":"Claudio","family":"Mirabello","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology, Link\u00f6ping University , SE-581 83 Link\u00f6ping,","place":["Sweden"]},{"name":"National Bioinformatics Infrastructure Sweden, Science for Life Laboratory , Link\u00f6ping University , SE-581 83 Link\u00f6ping,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3772-8279","authenticated-orcid":false,"given":"Bj\u00f6rn","family":"Wallner","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology, Link\u00f6ping University , SE-581 83 Link\u00f6ping,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,9,30]]},"reference":[{"key":"2024101105190064100_btae586-B1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2024101105190064100_btae586-B2","doi-asserted-by":"crossref","first-page":"e0161879","DOI":"10.1371\/journal.pone.0161879","article-title":"DockQ: a quality measure for protein-protein docking models","volume":"11","author":"Basu","year":"2016","journal-title":"PLoS One"},{"key":"2024101105190064100_btae586-B3","doi-asserted-by":"crossref","first-page":"i262","DOI":"10.1093\/bioinformatics\/btw257","article-title":"Finding correct protein\u2013protein docking models using ProQDock","volume":"32","author":"Basu","year":"2016","journal-title":"Bioinformatics"},{"key":"2024101105190064100_btae586-B4","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13321-019-0362-7","article-title":"Dockrmsd: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism","volume":"11","author":"Bell","year":"2019","journal-title":"J Cheminform"},{"key":"2024101105190064100_btae586-B5","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":"2024101105190064100_btae586-B6","doi-asserted-by":"crossref","first-page":"10480","DOI":"10.1038\/s41598-017-09654-8","article-title":"Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology","volume":"7","author":"Bertoni","year":"2017","journal-title":"Sci Rep"},{"key":"2024101105190064100_btae586-B7","doi-asserted-by":"crossref","first-page":"168540","DOI":"10.1016\/j.jmb.2024.168540","article-title":"CAPRI-Q: the CAPRI resource evaluating the quality of predicted structures of protein complexes","volume":"436","author":"Collins","year":"2024","journal-title":"J Mol Biol"},{"key":"2024101105190064100_btae586-B8","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1039\/b801115j","article-title":"Covalent radii revisited","volume":"21","author":"Cordero","year":"2008","journal-title":"Dalton Trans"},{"key":"2024101105190064100_btae586-B9","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1002\/prot.25815","article-title":"Introducing \u201cbest single template\u201d models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)","volume":"87","author":"Haas","year":"2019","journal-title":"Proteins Struct Funct Bioinf"},{"key":"2024101105190064100_btae586-B10","author":"Hagberg","year":"2008"},{"key":"2024101105190064100_btae586-B11","doi-asserted-by":"crossref","first-page":"eadl2528","DOI":"10.1126\/science.adl2528","article-title":"Generalized biomolecular modeling and design with RoseTTAFold All-Atom","volume":"384","author":"Krishna","year":"2024","journal-title":"Science"},{"key":"2024101105190064100_btae586-B12","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.1093\/bioinformatics\/btt473","article-title":"lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests","volume":"29","author":"Mariani","year":"2013","journal-title":"Bioinformatics"},{"key":"2024101105190064100_btae586-B13","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s13321-020-00455-2","article-title":"spyrmsd: symmetry-corrected RMSD calculations in Python","volume":"12","author":"Meli","year":"2020","journal-title":"J Cheminform"},{"key":"2024101105190064100_btae586-B14","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/prot.10393","article-title":"Assessment of blind predictions of protein-protein interactions: current status of docking methods","volume":"52","author":"M\u00e9ndez","year":"2003","journal-title":"Proteins"},{"key":"2024101105190064100_btae586-B15","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1093\/bioinformatics\/16.9.776","article-title":"MaxSub: an automated measure to assess the quality of protein structure predictions","volume":"16","author":"Siew","year":"2000","journal-title":"Bionformatics"},{"key":"2024101105190064100_btae586-B16","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1002\/prot.26612","article-title":"Assessment of the assessment\u2014all about complexes","volume":"91","author":"Studer","year":"2023","journal-title":"Proteins"},{"key":"2024101105190064100_btae586-B17","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1093\/bioinformatics\/btu739","article-title":"UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches","volume":"31","author":"Suzek","year":"2015","journal-title":"Bioinformatics"},{"key":"2024101105190064100_btae586-B18","doi-asserted-by":"crossref","first-page":"3370","DOI":"10.1093\/nar\/gkg571","article-title":"LGA: a method for finding 3D similarities in protein structures","volume":"31","author":"Zemla","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2024101105190064100_btae586-B19","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1038\/s41592-022-01585-1","article-title":"US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes","volume":"19","author":"Zhang","year":"2022","journal-title":"Nat Methods"},{"key":"2024101105190064100_btae586-B20","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Zhang","year":"2004","journal-title":"Proteins Struct Funct Bioinf"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae586\/59460026\/btae586.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/10\/btae586\/59716454\/btae586.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/10\/btae586\/59716454\/btae586.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,11]],"date-time":"2024-10-11T01:19:15Z","timestamp":1728609555000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae586\/7796530"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,9,30]]},"references-count":20,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2024,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae586","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.05.28.596225","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,10]]},"published":{"date-parts":[[2024,9,30]]},"article-number":"btae586"}}