{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T14:17:37Z","timestamp":1760710657253,"version":"3.37.3"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,6,25]],"date-time":"2021-06-25T00:00:00Z","timestamp":1624579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61732012","61822306","61861146002"],"award-info":[{"award-number":["61732012","61822306","61861146002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004826","name":"Beijing Natural Science Foundation","doi-asserted-by":"publisher","award":["JQ19019"],"award-info":[{"award-number":["JQ19019"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2018AAA0100100"],"award-info":[{"award-number":["2018AAA0100100"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Protein remote homology detection is a challenging task for the studies of protein evolutionary relationships. PSI-BLAST is an important and fundamental search method for detecting homology proteins. Although many improved versions of PSI-BLAST have been proposed, their performance is limited by the search processes of PSI-BLAST.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>For further improving the performance of PSI-BLAST for protein remote homology detection, a supervised two-layer search framework based on PSI-BLAST (S2L-PSIBLAST) is proposed. S2L-PSIBLAST consists of a two-level search: the first-level search provides high-quality search results by using SMI-BLAST framework and double-link strategy to filter the non-homology protein sequences, the second-level search detects more homology proteins by profile-link similarity, and more accurate ranking lists for those detected protein sequences are obtained by learning to rank strategy. Experimental results on the updated version of Structural Classification of Proteins-extended benchmark dataset show that S2L-PSIBLAST not only obviously improves the performance of PSI-BLAST, but also achieves better performance on two improved versions of PSI-BLAST: DELTA-BLAST and PSI-BLASTexB.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/bliulab.net\/S2L-PSIBLAST.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab472","type":"journal-article","created":{"date-parts":[[2021,6,24]],"date-time":"2021-06-24T11:10:35Z","timestamp":1624533035000},"page":"4321-4327","source":"Crossref","is-referenced-by-count":8,"title":["S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection"],"prefix":"10.1093","volume":"37","author":[{"given":"Xiaopeng","family":"Jin","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1012-5301","authenticated-orcid":false,"given":"Qing","family":"Liao","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3685-9469","authenticated-orcid":false,"given":"Bin","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Harbin Institute of Technology , Shenzhen, Guangdong 518055, China"},{"name":"School of Computer Science and Technology, Beijing Institute of Technology , Beijing 100081, China"},{"name":"Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology , Beijing 100081, China"}]}],"member":"286","published-online":{"date-parts":[[2021,6,25]]},"reference":[{"key":"2023061310482578400_btab472-B1","doi-asserted-by":"crossref","first-page":"13814","DOI":"10.1073\/pnas.0405612101","article-title":"Comparative homology agreement search: an effective combination of homology-search methods","volume":"101","author":"Alam","year":"2004","journal-title":"Proc. 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