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After the nucleotide base composition, the dinucleotide is the smallest unit of RNA sequence information and many RNA-binding proteins simply bind to regions enriched in one dinucleotide. Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferences could be identified. Using a standard approach to represent protein subsequences by their evolutionary profile, we trained neural networks to predict multiclass target vectors corresponding to 16 possible contacting dinucleotide subsequences. In the cross-validation experiments, the accuracies of the optimum network, measured as areas under the curve (AUC) of the receiver operating characteristic (ROC) graphs, were in the range of 65-80%.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Dinucleotide-specific contact predictions have also been extended to the prediction of interacting protein and RNA fragment pairs, which shows the applicability of this method to predict targets of RNA-binding proteins. A web server predicting the 16-dimensional contact probability matrix directly from a user-defined protein sequence was implemented and made available at: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/tardis.nibio.go.jp\/netasa\/srcpred\" ext-link-type=\"uri\">http:\/\/tardis.nibio.go.jp\/netasa\/srcpred<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s13-s5","type":"journal-article","created":{"date-parts":[[2011,12,2]],"date-time":"2011-12-02T05:05:33Z","timestamp":1322802333000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Prediction of dinucleotide-specific RNA-binding sites in proteins"],"prefix":"10.1186","volume":"12","author":[{"given":"Michael","family":"Fernandez","sequence":"first","affiliation":[]},{"given":"Yutaro","family":"Kumagai","sequence":"additional","affiliation":[]},{"given":"Daron M","family":"Standley","sequence":"additional","affiliation":[]},{"given":"Akinori","family":"Sarai","sequence":"additional","affiliation":[]},{"given":"Kenji","family":"Mizuguchi","sequence":"additional","affiliation":[]},{"given":"Shandar","family":"Ahmad","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,11,30]]},"reference":[{"key":"4921_CR1","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/S0959-440X(02)00323-8","volume":"12","author":"K Hall","year":"2002","unstructured":"Hall K: RNA-protein interactions. 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