Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights

By Philip M. Kim, Long J. Lu, Yu Xia, Mark Gerstein. Science, 2006

483 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8b06d311e1e75916b60992ade972d145ac12c762

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In Molecular Biology

Citations in the corpus

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality (2008, methodology): “Here we discuss how our findings fit the results reported in two such studies [35,36].”
Computational approaches for detecting protein complexes from protein interaction networks: a survey (2010, background): “Complex detection by considering exclusive or cooperative interactions Two adjacent interactions (those with a common protein) may be mutually exclusive [ 73 ,74] due to the overlapping binding interfaces on the common protein.”
CORUM: the comprehensive resource of mammalian protein complexes—2009 (2007, background): “Bioinformatics analysis of protein–protein interaction (PPI) datasets revealed that protein complex subunits are stronger evolutionary conserved and show a higher essentiality than proteins from other interactions (4).”
A core-attachment based method to detect protein complexes in PPI networks (2009, background): “Recent studies demonstrate that proteins structures and binding interfaces [46,47] are of help to address the above issue.”
Interactome3D: adding structural details to protein networks (2013, background): “…a more rational analysis of exposed disease-causing mutations 6,7 ; the design of experiments to disrupt an interaction and perturb systems where interactions are involved 8 ; and distinction between ‘singlish’ and multi-interface hubs, providing hints for understanding network dynamics 9 .”
Docking and scoring protein complexes: CAPRI 3rd Edition (2007, background): “3 Unfortunately, however, protein assemblies are still poorly represented in the protein data bank (PDB).”
CORUM: the comprehensive resource of mammalian protein complexes (2007, background): “They exhibit a higher essentiality, are to a large extent co-expressed and evolutionally stronger conserved than other proteins (8,9).”
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners (2008, background): “Additional evidence for the importance of disorder for highly connected hub proteins comes from a structurebased study of the yeast protein interaction network [51].”
Three-dimensional reconstruction of protein networks provides insight into human genetic disease (2012, methodology): “Next, we structurally resolved the interfaces of these interactions using a homology modeling approach 16 .”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…of each interacting node aiming to construct the 3D structure of the whole interactome, and discriminating between parallel and sequential interactions (Kim et al., 2006; Prieto & De Las Rivas, 2010; Bhardwaj et al., 2011; Clarke et al., 2012; Pache & Aloy, 2012; Sanchez Claros & Tramontano, 2012).”