A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules

By A. Tong, B. Drees, G. Nardelli, Gary D. Bader, Barbara Brannetti, L. Castagnoli, M. Evangelista, S. Ferracuti, Bryce P. Nelson, S. Paoluzi and 6 more. Science, 2001

735 citations recorded by the source corpus.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6015ab664628c7d3d9efc0258ae246ba7a848c75

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Citations in the corpus

Inference of gene regulatory networks and compound mode of action from time course gene expression profiles (2006, methodology): “Different experimental and computational methods have been proposed to tackle the network identification problem (Tong et al., 2002; Lee et al., 2002; Ideker et al., 2001; Davidson et al., 2002; Arkin et al., 1997; Yeung et al., 2002).”
Gaining confidence in high-throughput protein interaction networks (2004, neutral): “dtd" [ ]> Protein-protein interactions identified by high-throughput yeast two-hybrid screens (Y2H”
An automated method for finding molecular complexes in large protein interaction networks (2003, positive): “We previously published a simple graph theory method that identified a functional protein complex around the yeast protein Las17 that is involved in actin cytoskeleton rearrangement [ 10 ].”
Computational Alanine Scanning of Protein-Protein Interfaces (2004, methodology): “Protein-protein interactions are key components of all signal transduction processes, mediating the integration of linear pathways into the often complex interaction networks revealed by recent genome-scale studies (1).”
Subcellular localization of the yeast proteome. (2002, methodology): “Chromatography-coupled mass spectrometry (Gygi et al. 1999; Washburn et al. 2001), large-scale two-hybrid screens (Uetz et al. 2000; Ito et al. 2001; Tong et al. 2002), immunoprecipitation/mass spectrometric analysis of protein complexes (Gavin et al. 2002; Ho et al. 2002), and protein microarray…”
Computational approaches for detecting protein complexes from protein interaction networks: a survey (2010, background): “The main line of these researches is based on the observation that densely connected regions in the PPI networks often correspond to actual protein complexes [ 15 ], suggesting the identities of protein complexes can be revealed as tight-knitted substructures in protein-protein interaction maps [16]”
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, methodology): “(B) The PONDR VL-XT prediction for Las17p is plotted along with bars representing the positions of the WASP homology domain 1 (N-terminal orange bar), WASP homology domain 2 (C-terminal orange bar), poly-proline regions (green bars), and a predicted α-MoRF (blue bar). The number of interaction partn”