Structural systems biology: modelling protein interactions

By Patrick Aloy, Robert B. Russell. Nature reviews. Molecular cell biology, 2006

342 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a6b8c731d1fb7b1f0d3d2a9c415e82e7033a5ff5

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Citations in the corpus

Inter-residue, inter-protein and inter-family coevolution: bridging the scales (2017, background): “to what is called “structural systems biology” [42], or what could be called a structurally resolved, conserved interactome.”
FireDock: a web server for fast interaction refinement in molecular docking (2008, background): “( 3 ) Scoring and ranking: This final ranking stage attempts to identify the near-native refined solutions.”
Templates are available to model nearly all complexes of structurally characterized proteins (2012, background): “A fraction of the PPI for which we failed to find a template may be false positives, which are frequent in existing databases (24), and conversely, not all structures of the complexes built by the structure alignment will be correct.”
Contacts-based prediction of binding affinity in protein–protein complexes (2015, background): “…indeed an urgent need as it offers great opportunities not only to control interactions and develop innovative therapeutics ( Keskin et al., 2005 ; Aloy and Russell, 2006 ; Beltrao et al., 2007 ; Kiel et al., 2008 ; Dell’Orco, 2009 ), but also for other applications such as protein engineering (…”
Recent progress and future directions in protein-protein docking. (2008, neutral): “1389-2037/08 $55.00+.00 © 2008 Bentham Science Publishers Ltd. Keywords: Protein-protein docking, protein-protein interactions, docking algorithms, data-driven docking, molecular dynamics, protein structure databases, protein interface prediction, CAPRI.”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, neutral): “Although structure based methods for predicting protein-protein interactions might have a rather high noise level, accuracy comparable to other high-throughput methods can be achieved in combination with orthogonal information (Aloy and Russell, 2006; Zhang et al., 2012).”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, neutral): “As such, there is a pressing need to fill this ever-growing gap with models derived through computational means such as docking [38-45] and post-docking analysis [46,47].”