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- W2140287337 abstract "High-throughput proteomics has allowed for the drafting of large Protein-Interaction Networks and systems biology devotes a constant effort in the statistical analysis of these. PPIN derived from large-scale experiments portrait a global picture of proteins connectivity and offer an intricate and complex picture of the extracted interactions. The detailed analysis of a particular cellular function may benefit from the study of smaller and accurately selected sub-networks, containing high confidence interactions resulting from the cross-mapping of multiple sources of information for the nodes such as tissue-specific expression data, gene expression data, domain profiles and structural information. We call these extracted networks Sub-Networks Knowledge. Analysis of these SNKs provides the basis for the identification of fundamental components of the network and of specific pathways associated with the studied phenomenon that can be targeted to speed-up experimental screening and design new experiments. By reducing further the scale of details analysed in a given PPIN, one could focus only on special proteins in the network, like the multi-partner ones, called ‘hubs’. In particular, we concentrated on protein hubs that have a 3D-structure and on the characterization of their conformational dynamics and flexibility of the multiple interfaces. A large-scale survey of the intrinsic dynamics of protein interfaces has been done using a dataset of 340 proteins classified according to the different number of partners. Conformational ensembles were generated using the coarse-grained method tCONCOORD and the protein interfaces were identified with the POPSCOMP [1] method and characterized by analyzing the amino acid composition and conservation, the secondary structure content and the promiscuity of binding. A local measure of the interface “plasticity” was also obtained using our Structural Alphabet [2]. [1] Kleinjung J, Fraternali F. Nucleic Acids Res. 2005, 33:W342. [2] Pandini A, Fornili A, Kleinjung J. BMC Bioinformatics 2010, 11:97." @default.
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- W2140287337 date "2012-01-01" @default.
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- W2140287337 title "A Multiscale View of Protein-Protein Interactions" @default.
- W2140287337 doi "https://doi.org/10.1016/j.bpj.2011.11.1005" @default.
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