SH2 Domains pp 77-81 | Cite as

SH2 Ligand Prediction–Guidance for In-Silico Screening

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1555)

Abstract

Systematic identification of binding partners for SH2 domains is important for understanding the biological function of the corresponding SH2 domain-containing proteins. Here, we describe two different web-accessible computer programs, SMALI and DomPep, for predicting binding ligands for SH2 domains. The former was developed using a Scoring Matrix method and the latter based on the Support Vector Machine model.

Key words

SH2 SH2-peptide interactions Ligand prediction SMALI DomPep 

References

  1. 1.
    Liu BA et al (2006) The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell 22(6):851–868CrossRefPubMedGoogle Scholar
  2. 2.
    Huang H et al (2008) Defining the specificity space of the human SRC homology 2 domain. Mol Cell Proteomics 7(4):768–784CrossRefPubMedGoogle Scholar
  3. 3.
    Li L et al (2008) Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. Nucleic Acids Res 36(10):3263–3273CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Songyang Z, Cantley LC (1998) The use of peptide library for the determination of kinase peptide substrates. Methods Mol Biol 87:87–98PubMedGoogle Scholar
  5. 5.
    Yaffe MB et al (2001) A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat Biotechnol 19(4):348–353CrossRefPubMedGoogle Scholar
  6. 6.
    Li L et al (2011) DomPep—a general method for predicting modular domain-mediated protein-protein interactions. PLoS One 6(10):e25528CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Rodriguez M et al (2004) An oriented peptide array library (OPAL) strategy to study protein-protein interactions. J Biol Chem 279(10):8802–8807CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Biochemistry, Schulich School of Medicine and DentistryWestern UniversityLondonCanada
  2. 2.Children’s Health Research InstituteLondonCanada
  3. 3.Medical College of Qingdao UniversityQingdaoChina

Personalised recommendations