A motif-based profile scanning approach for genome-wide prediction of signaling pathways

By Michael B. Yaffe, G. Leparc, J. Lai, T. Obata, Stefano Volinia, Lewis C. Cantley. Nature Biotechnology, 2001

556 citations recorded by the source corpus.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/ced21c9721e29e64a24edc1977523ddbd39b21e7

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Citations in the corpus

Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. (2002, background): “AVO1, AVO2, and AVO3 all immunoprecipitated with AVO3 protein contains a RasGEFN domain between each other, but none of these proteins immunoprecipiamino acids 991 and 1047 (Yaffe et al., 2001).”
GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S (2008, background): “Numerous mechanisms have also been proposed to account for the specificity for PK recognition, such as subcellular co-localization of PKs with their substrates, co-complex, or interacting directly (28–30).”
Cytokine stimulation of energy expenditure through p38 MAP kinase activation of PPARgamma coactivator-1. (2001, methodology): “(Yaffe et al., 2001), identified half-life of PGC-1 protein by inhibiting its degradation. three clear consensus p38 MAPK phosphorylation sites, The molecular mechanisms or events underlying this T262, S265, and T298 (Figure 3A).”
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs (2003, methodology): “edu) is a computational tool built on experimental binding and/or substrate information from oriented peptide library screening (9–13) and phage display experiments (14), together with detailed biochemical characterization to derive a weight matrix-based scoring algorithm that predicts protein–prote”
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins (2003, background): “ELM is already the largest collection of linear motifs, followed by PROSITE and Scansite (32).”
Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles (2015, methodology): “Using this as a reference, we interrogated the human proteome (Yaffe et al., 2001), identifying 1,566 similar sequences (Figure 6C).”
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins (2004, unknown): “Phosphorylation site predictors such as the CBS predictor NetPhos [4] based on artificial neural networks [5,6], or Scansite [7] based on peptide library derived position-specific scoring matrices (PSSM) [ 8 ] have gone some way to allowing molecular biologists to identify potential kinase substrate”
Mechanisms of specificity in protein phosphorylation (2007, background): “Genome mining for proteins that contain these consensus phosphorylation sites is useful to predict whether a substrate is phosphorylated by a kinase of interes”
Scaffolding Adapter Grb2-Associated Binder 2 Requires Syk to Transmit Signals from FcεRI1 (2006, result): “This result is consistent with the predication by Scansite (41) that the cytoplasmic tail of Fc RI only contains tyrosine-containing motifs (Tyr217, Tyr223, and Tyr227) that may bind the Shc SH2 domain.”