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However, predicting domain targets by motif sequence alone without considering other genomic and structural information has been shown to be lacking in accuracy.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed an efficient search algorithm to scan the target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder. The integration is performed using na\u00efve Bayes and a training set of validated experiments.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>By integrating a variety of biologically relevant features to predict domain targets, we demonstrated a notably improved prediction of modular protein domain targets. Combined with emerging high-resolution data of domain specificities, we believe that our approach can assist in the reconstruction of many signaling pathways.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-243","type":"journal-article","created":{"date-parts":[[2010,5,12]],"date-time":"2010-05-12T06:13:59Z","timestamp":1273644839000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains"],"prefix":"10.1186","volume":"11","author":[{"given":"Hugo YK","family":"Lam","sequence":"first","affiliation":[]},{"given":"Philip M","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Janine","family":"Mok","sequence":"additional","affiliation":[]},{"given":"Raffi","family":"Tonikian","sequence":"additional","affiliation":[]},{"given":"Sachdev S","family":"Sidhu","sequence":"additional","affiliation":[]},{"given":"Benjamin E","family":"Turk","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Snyder","sequence":"additional","affiliation":[]},{"given":"Mark B","family":"Gerstein","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,5,11]]},"reference":[{"issue":"6967","key":"3700_CR1","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nature02178","volume":"426","author":"A Zarrinpar","year":"2003","unstructured":"Zarrinpar A, Park SH, Lim WA: Optimization of specificity in a cellular protein interaction network by negative selection. 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