A motif-based profile scanning approach for genome-wide prediction of signaling pathways
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Summary
A peptide library-based searching algorithm that identifies sequence motifs likely to bind to specific protein domains such as 14-3-3, SH2, and SH3 domains, or likely to be phosphorylated by specific protein kinases such as Src and AKT is described.
- Type
- article
- Published
- 2001-04-01
- Cited by
- 553
- References
- 33
- OpenAlex
- https://openalex.org/W1493799579
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:22637369
Keywords
Computational biology, Proteome, Sequence motif, Biology, Drug discovery
References
- Hierarchy of binding sites for Grb2 and Shc on the epidermal growth factor receptor
- Akt phosphorylation of BAD couples survival signals to the cell-intrinsic death machinery.
- Autophosphorylation and protein kinase C phosphorylation of the epidermal growth factor receptor. Effect on tyrosine kinase activity and ligand binding affinity.
- Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide
- A combined algorithm for genome-wide prediction of protein function
- Role of threonine residues in regulation of the epidermal growth factor receptor by protein kinase C and mitogen-activated protein kinase.
- Mapping specificity determinants for protein-protein association using protein fusions and random peptide libraries.
- SH2 domains prevent tyrosine dephosphorylation of the EGF receptor: identification of Tyr992 as the high‐affinity binding site for SH2 domains of phospholipase C gamma.
- The phosphotyrosine interaction domain of Shc binds an LXNPXY motif on the epidermal growth factor receptor
- Protein kinase C phosphorylation of the EGF receptor at a threonine residue close to the cytoplasmic face of the plasma membrane
- PhosphoBase, a database of phosphorylation sites: release 2.0
- Improving the sensitivity of the sequence profile method
- Protein modules and signalling networks
- Recognition of Unique Carboxyl-Terminal Motifs by Distinct PDZ Domains
- Three-dimensional structure of the tyrosine kinase c-Src
- The use of gene clusters to infer functional coupling.
- The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
- Conformation of amino acid side-chains in proteins.
- Peptide and Protein Library Screening Defines Optimal Substrate Motifs for AKT/PKB*
- Basic local alignment search tool.
Cited by
- PKB/AKT: functional insights from genetic models
- Identification of the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the phosphoinositide 3-kinase/akt pathway.
- Molecular characterization of the murine Slc26a6 anion exchanger: functional comparison with Slc26a1.
- Organization of cell–regulatory systems through modular–protein–interaction domains
- Transcriptional regulation by the MAP kinase signaling cascades.
- A Novel Proteomic Screen for Peptide-Protein Interactions*
- Convergent evolution of strigiform and caprimulgiform dark-activity is supported by phylogenetic analysis using the arylalkylamine N-acetyltransferase (Aanat) gene.
- Phosphoinositide 3-Kinase C2beta regulates cytoskeletal organization and cell migration via Rac-dependent mechanisms.
- Reverse interactomics: decoding protein-protein interactions with combinatorial peptide libraries.
- Fission yeast TORC1 regulates phosphorylation of ribosomal S6 proteins in response to nutrients and its activity is inhibited by rapamycin
- Yeast two-hybrid junk sequences contain selected linear motifs
- Design and data analysis of kinome microarrays
- How SH3 domains recognize proline.
- Efficient Algorithms for Improving the Accuracy in Motifs Prediction
- K-Nearest Neighbor Classifier Ensemble for Prediction of Phosphorylation Sites
- Enhanced prediction of conformational flexibility and phosphorylation in proteins.
- AKT in Differential miRNA Processing in Prostate Carcinoma
- Protéomique fonctionnelle de la signalisation de la kinase AKT dans le cancer du sein
- Informatics tools for the analysis and assignment of phosphorylation status in proteomics
- Controlling substrate specificity in protein kinases through chemical clamping
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