{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T16:40:24Z","timestamp":1717692024998},"reference-count":34,"publisher":"World Scientific Pub Co Pte Lt","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,8]]},"abstract":"<jats:p> Protein fold classification is a challenging task strongly associated with the determination of proteins' structure. In this work, we tested an optimization strategy on a Markov chain and a recently introduced Hidden Markov Model (HMM) with reduced state-space topology. The proteins with unknown structure were scored against both these models. Then the derived scores were optimized following a local optimization method. The Protein Data Bank (PDB) and the annotation of the Structural Classification of Proteins (SCOP) database were used for the evaluation of the proposed methodology. The results demonstrated that the fold classification accuracy of the optimized HMM was substantially higher compared to that of the Markov chain or the reduced state-space HMM approaches. The proposed methodology achieved an accuracy of 41.4% on fold classification, while Sequence Alignment and Modeling (SAM), which was used for comparison, reached an accuracy of 38%. <\/jats:p>","DOI":"10.1142\/s0219720014500164","type":"journal-article","created":{"date-parts":[[2014,6,18]],"date-time":"2014-06-18T22:32:44Z","timestamp":1403130764000},"page":"1450016","source":"Crossref","is-referenced-by-count":4,"title":["Assessment of optimized Markov models in protein fold classification"],"prefix":"10.1142","volume":"12","author":[{"given":"Christos","family":"Lampros","sequence":"first","affiliation":[{"name":"Department of Materials Science and Engineering, Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, GR 45110 Ioannina, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Simos","sequence":"additional","affiliation":[{"name":"Department of Biological Applications and Technology, University of Ioannina, GR 45110 Ioannina, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Themis P.","family":"Exarchos","sequence":"additional","affiliation":[{"name":"Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, FORTH, University of Ioannina, GR 45110 Ioannina, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Konstantinos P.","family":"Exarchos","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Engineering, Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, GR 45110 Ioannina, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Costas","family":"Papaloukas","sequence":"additional","affiliation":[{"name":"Department of Biological Applications and Technology, University of Ioannina, GR 45110 Ioannina, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitrios I.","family":"Fotiadis","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Engineering, Unit of Medical Technology and Intelligent Information Systems, University of Ioannina, GR 45110 Ioannina, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2014,8,25]]},"reference":[{"key":"rf1","volume-title":"Proteins: Structure and Function","author":"Whitford D.","year":"2005"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2009.03.008"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0407152101"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19990701)36:1<68::AID-PROT6>3.0.CO;2-1"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(1999)37:3+<88::AID-PROT13>3.0.CO;2-3"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(1999)37:3+<149::AID-PROT20>3.0.CO;2-H"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2008.02.004"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1007\/s00214-010-0799-2"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1126\/science.1853201"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(1997)1+<129::AID-PROT17>3.0.CO;2-Q"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2005.24"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-14"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0017215"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr367"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti629"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10369"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2006.10.014"},{"key":"rf20","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2009.07.007"},{"key":"rf21","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0115"},{"key":"rf22","doi-asserted-by":"publisher","DOI":"10.1504\/IJDMB.2013.055507"},{"key":"rf23","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22324"},{"key":"rf24","doi-asserted-by":"publisher","DOI":"10.1016\/j.neucom.2011.04.033"},{"key":"rf25","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2007.05.004"},{"key":"rf26","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2010.01.005"},{"key":"rf27","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2013.05.017"},{"key":"rf28","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492"},{"key":"rf29","volume":"2","author":"Lin H. 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