Interrogating protein interaction networks through structural biology

By Patrick Aloy, Robert B. Russell. Proceedings of the National Academy of Sciences of the United States of America, 2002

331 citations recorded by the source corpus.

Subfields: Cell Biology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c903c0948ea4282d3e2759ec0cf2cb0afe642478

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Citations in the corpus

3did: a catalog of domain-based interactions of known three-dimensional structure (2013, methodology): “Finally we assign a z-score to the DDIs [based on (26,27)].”
New benchmark metrics for protein-protein docking methods (2011, methodology): “In TB approaches,10–15 one first builds a homology model based on a solved template structure, and then refines the model.”
Structure-based prediction of protein-protein interactions on a genome-wide scale (2012, background): “We validated two previously uncharacterized interactions between the special AT-rich sequence-binding protein SATB2 and the Emerin ‘proteome’ complex 32, and one involving the pre-mRNA-processing factor PRPF19 and the centromere chromatin complex (Supplemen-taryFig.13).”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, unknown): “16,17 Homology modeling 18 and multi-meric threading 19 approaches, which apply the knowledge learned from a known complex structure to the component (apo) homologs and examine the predicted contact residues using a speciﬁc potential function, are able to predict interaction partners of a protein…”
Template-based structure modeling of protein-protein interactions (2013, methodology): “Most TBM methods, including InterPreTS [44,48], MULTIPROSPECTOR [24], HOMBACOP [25], HOMCOS [45,49], Struct2Net [26,50] and Coev2Net [47 ], rely on a complex template library to predict the chain orientations (quaternary structure) and the backbone framework of the targets.”
ISIS: interaction sites identified from sequence (2007, background): “Our analysis of protein interfaces at the sequence level suggested that most interacting residues have other interacting residues in their sequence neighborhood (Ofran”
Recent progress and future directions in protein-protein docking. (2008, methodology): “In a recent adaptation of the SPF approach, Sumikoshi et al. [64] perform very fast low order N=10–12 soft docking correlations.”
Docking, scoring, and affinity prediction in CAPRI (2013, background): “8,9 But progress has been slow, because protein assemblies remain poorly represented in the Protein Data Bank (PDB).”
Interactome: gateway into systems biology. (2005, background): “Integrating other types of data (133), either data from alternative PPI approaches (101,134,135), or data from altogether different functional genomics approaches (17,120,129,136–138), or both (79,96,102), with interactome maps is the most effective way to assign function to uncharacterized proteins”
Protein–Protein Interaction Hotspots Carved into Sequences (2007, background): “That is, no protein in the test set could have been modeled by any protein in the development sets by homology-based predictions [43,44].”