Protein interface conservation across structure space

By Qiangfeng Cliff Zhang, Donald Petrey, Raquel Norel, Barry Honig. 2010

155 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, positive): “The approach can be scaled to entire genomes and applied to binary as well as to higher-order protein assemblies (17,18,22,23).”
Templates are available to model nearly all complexes of structurally characterized proteins (2012, result): “Our observation correlates with the conclusions of the study by Honig and co-workers (23) on the completeness of current structural databases of protein – protein interactions.”
Dockground: A comprehensive data resource for modeling of protein complexes (2018, background): “32 Evolutionary conserved surface patches may yield similar binding modes for otherwise dissimilar proteins, 33,34 which implies that docking can also be performed by the structure alignment between the target proteins and the interface parts of the templates.”
Template-based structure modeling of protein-protein interactions (2013, background): “Rather than considering the structures of entire complexes, one can focus solely on the protein–protein interfaces, and examine how much they are covered by the current PDB [53 ,54 ].”
Structure-based Systems Biology for Analyzing Off-target Binding (2011, background): “Evolutionary and functional linkage between proteins can exist across fold space at the level of functional sites [39–41].”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, background): “Similarly, most protein–protein interaction interfaces remain well-conserved over time, at least for the case of stably bound protein partners located next to each other in protein complexes (38,39).”
Structure-based prediction of protein-protein interactions on a genome-wide scale (2012, background): “Most protein complexes in the PDB have structural neighbours that share binding properties 17 , and protein interface space may well be close to ‘complete’ in terms of the packing orientations of secondary structure elements 18 .”
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction (2021, background): “Nature Computational Science, 1(7), 462-469.”