{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T23:28:02Z","timestamp":1771716482151,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":139,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["R01GM081871"],"award-info":[{"award-number":["R01GM081871"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein\u2013RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein\u2013RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset.<\/jats:p>\n               <jats:p>Results: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein\u2013RNA structure-based models on an unprecedented scale.<\/jats:p>\n               <jats:p>Availability and Implementation: Software and models are freely available at http:\/\/rck.csail.mit.edu\/<\/jats:p>\n               <jats:p>Contact: \u00a0bab@mit.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw259","type":"journal-article","created":{"date-parts":[[2016,6,15]],"date-time":"2016-06-15T15:43:52Z","timestamp":1466005432000},"page":"i351-i359","source":"Crossref","is-referenced-by-count":81,"title":["RCK: accurate and efficient inference of sequence- and structure-based protein\u2013RNA binding models from RNAcompete data"],"prefix":"10.1093","volume":"32","author":[{"given":"Yaron","family":"Orenstein","sequence":"first","affiliation":[{"name":"1Computer Science and Artificial Intelligence Laboratory"}]},{"given":"Yuhao","family":"Wang","sequence":"additional","affiliation":[{"name":"1Computer Science and Artificial Intelligence Laboratory"}]},{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[{"name":"1Computer Science and Artificial Intelligence Laboratory"},{"name":"2Math Department, MIT, Cambridge, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,11]]},"reference":[{"key":"2023020112351449400_btw259-B1","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning","volume":"33","author":"Alipanahi","year":"2015","journal-title":"Nat. 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