{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T16:28:39Z","timestamp":1762100919100},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein.<\/jats:p>\n               <jats:p>Results: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations.<\/jats:p>\n               <jats:p>Availability and Implementation: Freely available on the web at www.bioinformatics.sussex.ac.uk\/PIRANHA or http:\/\/piranha.protein.osaka-u.ac.jp.<\/jats:p>\n               <jats:p>Contact: \u00a0s.jones@sussex.ac.uk.<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at the Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp257","type":"journal-article","created":{"date-parts":[[2009,4,24]],"date-time":"2009-04-24T00:25:34Z","timestamp":1240532734000},"page":"1492-1497","source":"Crossref","is-referenced-by-count":41,"title":["Protein function annotation from sequence: prediction of residues interacting with RNA"],"prefix":"10.1093","volume":"25","author":[{"given":"R. V.","family":"Spriggs","sequence":"first","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK and 2Research Centre for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y.","family":"Murakami","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK and 2Research Centre for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H.","family":"Nakamura","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK and 2Research Centre for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry and Biochemistry, School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK and 2Research Centre for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,4,23]]},"reference":[{"key":"2023013111584512100_B1","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1002\/prot.20441","article-title":"Combining prediction of secondary structure and solvent accessibility in proteins","volume":"59","author":"Adamczak","year":"2005","journal-title":"Proteins: Struct. 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