{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,26]],"date-time":"2023-09-26T16:01:47Z","timestamp":1695744107410},"reference-count":38,"publisher":"World Scientific Pub Co Pte Lt","issue":"05","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,10]]},"abstract":"<jats:p>A conserved epitope is an epitope retained by multiple strains of influenza as the key target of a broadly neutralizing antibody. Identification of conserved epitopes is of strong interest to help design broad-spectrum vaccines against influenza. Conservation score measures the evolutionary conservation of an amino acid position in a protein based on the phylogenetic relationships observed amongst homologous sequences. Here, Average Amino Acid Conservation Score (AAACS) is proposed as a method to identify HA's conserved epitopes. Our analysis shows that there is a clear distinction between conserved epitopes and nonconserved epitopes in terms of AAACS. This method also provides an excellent classification performance on an independent dataset. In contrast, alignment-based comparison methods do not work well for this problem, because conserved epitopes to the same broadly neutralizing antibody are usually not identical or similar. Location-based methods are not successful either, because conserved epitopes are located at both the less-conserved globular head (HA1) and the more-conserved stem (HA2). As a case study, two conserved epitopes on HA are predicted for the influenza A virus H7N9: One should match the broadly neutralizing antibodies CR9114 or FI6v3, while the other is new and requires validation by wet-lab experiments.<\/jats:p>","DOI":"10.1142\/s0219720014500231","type":"journal-article","created":{"date-parts":[[2014,8,12]],"date-time":"2014-08-12T06:20:34Z","timestamp":1407824434000},"page":"1450023","source":"Crossref","is-referenced-by-count":5,"title":["Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method"],"prefix":"10.1142","volume":"12","author":[{"given":"Jing","family":"Ren","sequence":"first","affiliation":[{"name":"Advanced Analytics Institute, Faculty of Engineering and Information Technology, University of Technology Sydney, P. O. Box 123, Broadway, NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Ellis","sequence":"additional","affiliation":[{"name":"School of Medical and Molecular Biosciences, University of Technology Sydney, P. O. Box 123, Broadway, NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinyan","family":"Li","sequence":"additional","affiliation":[{"name":"Advanced Analytics Institute and Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology Sydney, P. O. 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