{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,14]],"date-time":"2026-06-14T16:54:42Z","timestamp":1781456082815,"version":"3.54.1"},"reference-count":1,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,6,14]],"date-time":"2026-06-14T00:00:00Z","timestamp":1781395200000},"content-version":"vor","delay-in-days":44,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We thank MD Kazim Okan Dolu for their interest in our published work and for the opportunity to clarify several points regarding software versioning, benchmark independence, secondary-structure generation, binding-free-energy terminology, and negative-control design. We acknowledge that several descriptions in the original manuscript could be stated more precisely. These clarifications improve the transparency and reproducibility of the study, but do not affect the reported analyses or main conclusions.<\/jats:p>","DOI":"10.1093\/bib\/bbag309","type":"journal-article","created":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T11:51:05Z","timestamp":1779450665000},"source":"Crossref","is-referenced-by-count":0,"title":["Reply to \u201cLetter to the editor: methodological considerations in the benchmarking of AI-based protein\u2013aptamer complex prediction\u201d"],"prefix":"10.1093","volume":"27","author":[{"given":"Jiani","family":"Zhao","sequence":"first","affiliation":[{"name":"Department of Computer Science, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kha","family":"Tram","sequence":"additional","affiliation":[{"name":"Cytodiagnostics Inc. , 919 Fraser Dr Unit 11, Burlington L7L 4X8, Ontario ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongbin","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Chemistry , Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4873-6928","authenticated-orcid":false,"given":"Yifeng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","place":["Canada"]},{"name":"Department of Biological Sciences, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,14]]},"reference":[{"key":"2026061410250736700_ref1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbag206","article-title":"Comprehensive evaluation of artificial intelligence-empowered approaches for protein\u2013aptamer complex prediction","volume":"27","author":"Zhao","year":"2026","journal-title":"Brief Bioinform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/3\/bbag309\/68523225\/bbag309.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/3\/bbag309\/68523225\/bbag309.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,14]],"date-time":"2026-06-14T16:07:46Z","timestamp":1781453266000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag309\/8707709"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5]]},"references-count":1,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag309","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,5]]},"published":{"date-parts":[[2026,5]]},"article-number":"bbag309"}}