Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach.

ABSTRACT: Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct

SUBMITTER: Li L 

PROVIDER: S-EPMC2425477 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature