{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T08:12:00Z","timestamp":1763367120582},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Template-based modeling, the most successful approach for predicting protein 3D structure, often requires detecting distant evolutionary relationships between the target sequence and proteins of known structure. Developed for this purpose, fold recognition methods use elaborate strategies to exploit evolutionary information, mainly by encoding amino acid sequence into profiles. Since protein structure is more conserved than sequence, the inclusion of structural information can improve the detection of remote homology.<\/jats:p>\n               <jats:p>Results: Here, we present ORION, a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure. Our method uses the 16-state structural alphabet Protein Blocks, which provides an accurate 1D description of protein structure local conformations. ORION systematically outperforms PSI-BLAST and HHsearch on several benchmarks, including target sequences from the modeling competitions CASP8, 9 and 10, and detects \u223c10% more templates at fold and superfamily SCOP levels.<\/jats:p>\n               <jats:p>Availability: Software freely available for download at http:\/\/www.dsimb.inserm.fr\/orion\/.<\/jats:p>\n               <jats:p>Contact: \u00a0jean-christophe.gelly@univ-paris-diderot.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv462","type":"journal-article","created":{"date-parts":[[2015,8,8]],"date-time":"2015-08-08T01:01:16Z","timestamp":1438995676000},"page":"3782-3789","source":"Crossref","is-referenced-by-count":33,"title":["Improving protein fold recognition with hybrid profiles combining sequence and structure evolution"],"prefix":"10.1093","volume":"31","author":[{"given":"Yassine","family":"Ghouzam","sequence":"first","affiliation":[{"name":"1 Inserm U1134, Paris, France,"},{"name":"2 Universit\u00e9 Paris Diderot, Sorbonne Paris Cit\u00e9, UMR_S 1134, Paris, France,"},{"name":"3 Institut National de la Transfusion Sanguine, Paris, France and"},{"name":"4 Laboratory of Excellence GR-Ex, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guillaume","family":"Postic","sequence":"additional","affiliation":[{"name":"1 Inserm U1134, Paris, France,"},{"name":"2 Universit\u00e9 Paris Diderot, Sorbonne Paris Cit\u00e9, UMR_S 1134, Paris, France,"},{"name":"3 Institut National de la Transfusion Sanguine, Paris, France and"},{"name":"4 Laboratory of Excellence GR-Ex, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandre G.","family":"de Brevern","sequence":"additional","affiliation":[{"name":"1 Inserm U1134, Paris, France,"},{"name":"2 Universit\u00e9 Paris Diderot, Sorbonne Paris Cit\u00e9, UMR_S 1134, Paris, France,"},{"name":"3 Institut National de la Transfusion Sanguine, Paris, France and"},{"name":"4 Laboratory of Excellence GR-Ex, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Christophe","family":"Gelly","sequence":"additional","affiliation":[{"name":"1 Inserm U1134, Paris, France,"},{"name":"2 Universit\u00e9 Paris Diderot, Sorbonne Paris Cit\u00e9, UMR_S 1134, Paris, France,"},{"name":"3 Institut National de la Transfusion Sanguine, Paris, France and"},{"name":"4 Laboratory of Excellence GR-Ex, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,8,7]]},"reference":[{"key":"2023020202414095700_btv462-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023020202414095700_btv462-B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023020202414095700_btv462-B3","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1126\/science.1853201","article-title":"A method to identify protein sequences that fold into a known three-dimensional structure","volume":"253","author":"Bowie","year":"1991","journal-title":"Science"},{"key":"2023020202414095700_btv462-B4","doi-asserted-by":"crossref","first-page":"6073","DOI":"10.1073\/pnas.95.11.6073","article-title":"Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships","volume":"95","author":"Brenner","year":"1998","journal-title":"PNAS"},{"key":"2023020202414095700_btv462-B5","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1002\/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z","article-title":"Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks","volume":"41","author":"de Brevern","year":"2000","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B6","doi-asserted-by":"crossref","first-page":"2150","DOI":"10.1110\/ps.0306803","article-title":"A consensus view of fold space: combining SCOP, CATH, and the Dali domain dictionary","volume":"12","author":"Day","year":"2003","journal-title":"Protein Sci."},{"key":"2023020202414095700_btv462-B7","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"2023020202414095700_btv462-B8","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1002\/prot.10043","article-title":"A study on protein sequence alignment quality","volume":"46","author":"Elofsson","year":"2002","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B9","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0506s15","article-title":"Comparative protein structure modeling using Modeller","volume-title":"Curr Protoc Bioinformatics","author":"Eswar","year":"2006"},{"key":"2023020202414095700_btv462-B10","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1089\/cmb.2011.0236","article-title":"Statistical significance of threading scores","volume":"19","author":"Fayyaz Movaghar","year":"2011","journal-title":"J. Comput. Biol."},{"key":"2023020202414095700_btv462-B11","first-page":"300","article-title":"Assessing the performance of fold recognition methods by means of a comprehensive benchmark","author":"Fischer","year":"1996","journal-title":"Pac. Symp. Biocomput."},{"key":"2023020202414095700_btv462-B12","doi-asserted-by":"crossref","first-page":"W18","DOI":"10.1093\/nar\/gkr333","article-title":"iPBA: a tool for protein structure comparison using sequence alignment strategies","volume":"39","author":"Gelly`","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023020202414095700_btv462-B13","first-page":"141","article-title":"Measures of central tendency in rehabilitation research: what do they mean? Am","volume":"80","author":"Gonzales","year":"2001","journal-title":"J. Phys. Med. Rehabil."},{"key":"2023020202414095700_btv462-B14","doi-asserted-by":"crossref","first-page":"4355","DOI":"10.1073\/pnas.84.13.4355","article-title":"Profile analysis: detection of distantly related proteins","volume":"84","author":"Gribskov","year":"1987","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020202414095700_btv462-B15","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1093\/bioinformatics\/17.3.272","article-title":"PICASSO: generating a covering set of protein family profiles","volume":"17","author":"Heger","year":"2001","journal-title":"Bioinformatics"},{"key":"2023020202414095700_btv462-B16","first-page":"135","article-title":"Using substitution probabilities to improve position-specific scoring matrices","volume":"12","author":"Henikoff","year":"1996","journal-title":"Comput. Appl. Biosci."},{"key":"2023020202414095700_btv462-B17","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1016\/0022-2836(94)90032-9","article-title":"Position-based sequence weights","volume":"243","author":"Henikoff","year":"1994","journal-title":"J. Mol. Biol."},{"key":"2023020202414095700_btv462-B18","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1002\/prot.22458","article-title":"Structure is three to ten times more conserved than sequence\u2014a study of structural response in protein cores","volume":"77","author":"Illerg\u00e5rd","year":"2009","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B19","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/358086a0","article-title":"A new approach to protein fold recognition","volume":"358","author":"Jones","year":"1992","journal-title":"Nature"},{"key":"2023020202414095700_btv462-B20","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1007\/s12551-010-0036-1","article-title":"A short survey on protein blocks","volume":"2","author":"Joseph","year":"2010","journal-title":"Biophys. Rev."},{"key":"2023020202414095700_btv462-B21","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1093\/bioinformatics\/14.10.846","article-title":"Hidden Markov models for detecting remote protein homologies","volume":"14","author":"Karplus","year":"1998","journal-title":"Bioinformatics"},{"key":"2023020202414095700_btv462-B22","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1006\/jmbi.2000.3741","article-title":"Enhanced genome annotation using structural profiles in the program 3D-PSSM1","volume":"299","author":"Kelley","year":"2000","journal-title":"J. Mol. 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Biol."},{"key":"2023020202414095700_btv462-B25","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1142\/9789812778789_0002","article-title":"Protein fold recognition and threading","volume-title":"Computational Structural Biology: Methods and Applications 1st Edition","author":"McGuffin","year":"2008"},{"key":"2023020202414095700_btv462-B26","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1093\/bioinformatics\/btg185","article-title":"Probabilistic scoring measures for profile\u2013profile comparison yield more accurate short seed alignments","volume":"19","author":"Mittelman","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020202414095700_btv462-B27","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1002\/pro.5560071126","article-title":"HOMSTRAD: a database of protein structure alignments for homologous families","volume":"7","author":"Mizuguchi","year":"1998","journal-title":"Protein Sci."},{"key":"2023020202414095700_btv462-B28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/prot.22589","article-title":"Critical assessment of methods of protein structure prediction Round VIII","volume":"9","author":"Moult","year":"2009","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/prot.23200","article-title":"Critical assessment of methods of protein structure prediction (CASP)\u2014round IX","volume":"79","author":"Moult","year":"2011","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/prot.24452","article-title":"Critical assessment of methods of protein structure prediction (CASP) \u2014 round x","volume":"82","author":"Moult","year":"2014","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B31","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1006\/jmbi.1999.3233","article-title":"Benchmarking PSI-BLAST in genome annotation","volume":"293","author":"M\u00fcller","year":"1999","journal-title":"J. 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Biol."},{"key":"2023020202414095700_btv462-B33","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1002\/prot.20184","article-title":"Profile\u2013profile methods provide improved fold-recognition: a study of different profile\u2013profile alignment methods","volume":"57","author":"Ohlson","year":"2004","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B34","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1093\/nar\/gkg154","article-title":"Finding weak similarities between proteins by sequence profile comparison","volume":"31","author":"Panchenko","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023020202414095700_btv462-B35","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1006\/jmbi.1998.2221","article-title":"Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods","volume":"284","author":"Park","year":"1998","journal-title":"J. Mol. Biol."},{"key":"2023020202414095700_btv462-B36","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/0888-7543(91)90071-L","article-title":"Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms","volume":"11","author":"Pearson","year":"1991","journal-title":"Genomics"},{"key":"2023020202414095700_btv462-B37","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1186\/1471-2105-10-439","article-title":"svmPRAT: SVM-based protein residue annotation toolkit","volume":"10","author":"Rangwala","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020202414095700_btv462-B38","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1002\/prot.21662","article-title":"Assessment of CASP7 predictions in the high accuracy template-based modeling category","volume":"69","author":"Read","year":"2007","journal-title":"Proteins"},{"key":"2023020202414095700_btv462-B39","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nmeth.1818","article-title":"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment","volume":"9","author":"Remmert","year":"2012","journal-title":"Nat. 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Biol."},{"key":"2023020202414095700_btv462-B43","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM\u2013HMM comparison","volume":"21","author":"S\u00f6ding","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020202414095700_btv462-B44","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/j.sbi.2011.03.005","article-title":"Protein sequence comparison and fold recognition: progress and good-practice benchmarking","volume":"21","author":"S\u00f6ding","year":"2011","journal-title":"Curr. Opin. Struct. 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