{"id":"https://openalex.org/W7164768266","doi":"https://doi.org/10.1093/bib/bbag309","title":"Reply to \u201cLetter to the editor: methodological considerations in the benchmarking of AI-based protein\u2013aptamer complex prediction\u201d","display_name":"Reply to \u201cLetter to the editor: methodological considerations in the benchmarking of AI-based protein\u2013aptamer complex prediction\u201d","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7164768266","doi":"https://doi.org/10.1093/bib/bbag309","pmid":"https://pubmed.ncbi.nlm.nih.gov/42289046"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag309","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag309","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag309","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5135170658","display_name":"Jiani Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I186803428","display_name":"Brock University","ror":"https://ror.org/056am2717","country_code":"CA","type":"education","lineage":["https://openalex.org/I186803428"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jiani Zhao","raw_affiliation_strings":["Department of Computer Science, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","institution_ids":["https://openalex.org/I186803428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135140992","display_name":"Kha Tram","orcid":null},"institutions":[{"id":"https://openalex.org/I4210104087","display_name":"Cytodiagnostics (Canada)","ror":"https://ror.org/01bat1a85","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210104087"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Kha Tram","raw_affiliation_strings":["Cytodiagnostics Inc. , 919 Fraser Dr Unit 11, Burlington L7L 4X8, Ontario ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cytodiagnostics Inc. , 919 Fraser Dr Unit 11, Burlington L7L 4X8, Ontario ,","institution_ids":["https://openalex.org/I4210104087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000070759","display_name":"Hongbin Yan","orcid":"https://orcid.org/0000-0002-9087-0493"},"institutions":[{"id":"https://openalex.org/I186803428","display_name":"Brock University","ror":"https://ror.org/056am2717","country_code":"CA","type":"education","lineage":["https://openalex.org/I186803428"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Hongbin Yan","raw_affiliation_strings":["Department of Chemistry , Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry , Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","institution_ids":["https://openalex.org/I186803428"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033510515","display_name":"Yifeng Li","orcid":"https://orcid.org/0000-0002-4873-6928"},"institutions":[{"id":"https://openalex.org/I186803428","display_name":"Brock University","ror":"https://ror.org/056am2717","country_code":"CA","type":"education","lineage":["https://openalex.org/I186803428"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Yifeng Li","raw_affiliation_strings":["Department of Biological Sciences, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","Department of Computer Science, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,"],"raw_orcid":"https://orcid.org/0000-0002-4873-6928","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","institution_ids":["https://openalex.org/I186803428"]},{"raw_affiliation_string":"Department of Computer Science, Brock University , 1812 Sir Isaac Brock Way, St. Catharines L2S 3A1, Ontario ,","institution_ids":["https://openalex.org/I186803428"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033510515"],"corresponding_institution_ids":["https://openalex.org/I186803428"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.31220000982284546,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.31220000982284546,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.09009999781847,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.0843999981880188,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.9014999866485596},{"id":"https://openalex.org/keywords/transparency","display_name":"Transparency (behavior)","score":0.8288000226020813},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7376999855041504},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4629000127315521},{"id":"https://openalex.org/keywords/affect","display_name":"Affect (linguistics)","score":0.41609999537467957}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9014999866485596},{"id":"https://openalex.org/C2780233690","wikidata":"https://www.wikidata.org/wiki/Q535347","display_name":"Transparency (behavior)","level":2,"score":0.8288000226020813},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7376999855041504},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5939000248908997},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4629000127315521},{"id":"https://openalex.org/C2776035688","wikidata":"https://www.wikidata.org/wiki/Q1606558","display_name":"Affect (linguistics)","level":2,"score":0.41609999537467957},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.413100004196167},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.39899998903274536},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.37290000915527344},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.2809000015258789},{"id":"https://openalex.org/C42475967","wikidata":"https://www.wikidata.org/wiki/Q194292","display_name":"Operations research","level":1,"score":0.2732999920845032}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag309","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag309","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42289046","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42289046","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":"Letter"},{"id":"pmh:oai:pubmedcentral.nih.gov:13264833","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13264833/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag309","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag309","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":1,"referenced_works":["https://openalex.org/W7160148887"],"related_works":[],"abstract_inverted_index":{"We":[0,33],"thank":[1],"MD":[2],"Kazim":[3],"Okan":[4],"Dolu":[5],"for":[6,14],"their":[7],"interest":[8],"in":[9,38],"our":[10],"published":[11],"work":[12],"and":[13,30,52],"the":[15,39,50,55,61],"opportunity":[16],"to":[17],"clarify":[18],"several":[19,36],"points":[20],"regarding":[21],"software":[22],"versioning,":[23],"benchmark":[24],"independence,":[25],"secondary-structure":[26],"generation,":[27],"binding-free-energy":[28],"terminology,":[29],"negative-control":[31],"design.":[32],"acknowledge":[34],"that":[35],"descriptions":[37],"original":[40],"manuscript":[41],"could":[42],"be":[43],"stated":[44],"more":[45],"precisely.":[46],"These":[47],"clarifications":[48],"improve":[49],"transparency":[51],"reproducibility":[53],"of":[54],"study,":[56],"but":[57],"do":[58],"not":[59],"affect":[60],"reported":[62],"analyses":[63],"or":[64],"main":[65],"conclusions.":[66]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-15T00:00:00"}
