title: MOTIPS: automated motif analysis for predicting targets of modular protein domains.
abstract: BACKGROUND
  Many protein interactions, especially those involved in signaling, involve short linear motifs consisting of 5-10 amino acid residues that interact with modular protein domains such as the SH3 binding domains and the kinase catalytic domains. One straightforward way of identifying these interactions is by scanning for matches to the motif against all the sequences in a target proteome. However, predicting domain targets by motif sequence alone without considering other genomic and structural information has been shown to be lacking in accuracy.
  
  
  RESULTS
  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 naïve Bayes and a training set of validated experiments.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
authors.forename: Hugo Y K
authors.initials: HY
authors.lastname: Lam
authors.forename: Philip M
authors.initials: PM
authors.lastname: Kim
authors.forename: Janine
authors.initials: J
authors.lastname: Mok
authors.forename: Raffi
authors.initials: R
authors.lastname: Tonikian
authors.forename: Sachdev S
authors.initials: SS
authors.lastname: Sidhu
authors.forename: Benjamin E
authors.initials: BE
authors.lastname: Turk
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Mark B
authors.initials: MB
authors.lastname: Gerstein
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins; D020543:Proteome
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