A neural strategy for the inference of SH3 domain-peptide interaction specificity
نویسندگان
چکیده
منابع مشابه
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity
MOTIVATION Unravelling the rules underlying protein-protein and protein-ligand interactions is a crucial step in understanding cell machinery. Peptide recognition modules (PRMs) are globular protein domains which focus their binding targets on short protein sequences and play a key role in the frame of protein-protein interactions. High-throughput techniques permit the whole proteome scanning o...
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Extensive efforts have been devoted to determining the binding specificity of Src homology 3 (SH3) domains usually in a case-by-case manner. A generic structure-based model is necessary to decipher the protein recognition code of the entire domain family. In this study, we have developed a general framework that combines molecular modeling and a machine learning algorithm to capture the energet...
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Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decompos...
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SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide-domain pairs. The server can accept ...
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To explore the conservation of Src homology 3 (SH3) domain-mediated networks in evolution, we compared the specificity landscape of these domains among four yeast species, Saccharomyces cerevisiae, Ashbya gossypii, Candida albicans, and Schizosaccharomyces pombe, encompassing 400 million years of evolution. We first aligned and catalogued the families of SH3-containing proteins in these four sp...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2005
ISSN: 1471-2105
DOI: 10.1186/1471-2105-6-s4-s13