{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T21:22:15Z","timestamp":1745875335378},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"Abstract<\/jats:title>\n Motivation: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains.<\/jats:p>\n Results: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (\u03b1, \u03b2, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build and empirically compare our method. MoRFpred utilizes a novel design in which annotations generated by sequence alignment are fused with predictions generated by a Support Vector Machine (SVM), which uses a custom designed set of sequence-derived features. The features provide information about evolutionary profiles, selected physiochemical properties of amino acids, and predicted disorder, solvent accessibility and B-factors. Empirical evaluation on several datasets shows that MoRFpred outperforms related methods: \u03b1-MoRF-Pred that predicts \u03b1-MoRFs and ANCHOR which finds disordered regions that become ordered when bound to a globular partner. We show that our predicted (new) MoRF regions have non-random sequence similarity with native MoRFs. We use this observation along with the fact that predictions with higher probability are more accurate to identify putative MoRF regions. We also identify a few sequence-derived hallmarks of MoRFs. They are characterized by dips in the disorder predictions and higher hydrophobicity and stability when compared to adjacent (in the chain) residues.<\/jats:p>\n Availability: \u00a0http:\/\/biomine.ece.ualberta.ca\/MoRFpred\/; http:\/\/biomine.ece.ualberta.ca\/MoRFpred\/Supplement.pdf<\/jats:p>\n Contact: \u00a0lkurgan@ece.ualberta.ca<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts209","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i75-i83","source":"Crossref","is-referenced-by-count":309,"title":["MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins"],"prefix":"10.1093","volume":"28","author":[{"given":"Fatemeh Miri","family":"Disfani","sequence":"first","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"Wei-Lun","family":"Hsu","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"Marcin J.","family":"Mizianty","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"Christopher J.","family":"Oldfield","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"Bin","family":"Xue","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"A. Keith","family":"Dunker","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"Vladimir N.","family":"Uversky","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"},{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]},{"given":"Lukasz","family":"Kurgan","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, T6G 2V4, Canada, 2Center for Computational Biology and Bioinformatics and Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, 46202, USA 3Department of Molecular Medicine, University of South Florida, Tampa, 33612, USA and 4Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512392184800_B1","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":"2023012512392184800_B2","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1002\/prot.20240","article-title":"Principal eigenvector of contact matrices and hydrophobicity profiles in proteins","volume":"58","author":"Bastolla","year":"2005","journal-title":"Proteins"},{"key":"2023012512392184800_B3","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkl971","article-title":"The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data","volume":"35","author":"Berman","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512392184800_B4","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1016\/j.jmb.2004.05.046","article-title":"Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonucleaseRNase E","volume":"340","author":"Callaghan","year":"2004","journal-title":"J. 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