MOTIPS employs an efficient search algorithm to scan a 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.
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BMC Bioinformatics. 2010 May 11;11:243. doi: 10.1186/1471-2105-11-243.
MOTIPS: automated motif analysis for predicting targets of modular protein domains.
Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB.