Template-based structure modeling of protein-protein interactions

By András Szilágyi, Yang Zhang. 2013

164 citations recorded by the source corpus.

The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, positive): “Similar to comparative modelling of monomeric proteins, the information of a protein’s quaternary structure is transferred by homology to another one, and a model of the complex is obtained based on the structures of the interacting homologs, i.e. in-terologs, as templates (19–21).”
Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2 (2015, methodology): “Computational approaches for modeling protein-protein complex structures include ab-initio docking methods [3,4], homology-based methods based on the experimental structures of similar complexes [5-11], and integrative, information-driven methods [12], These approaches typically attempt to predict t”
Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus (2017, background): “tions can be modeled using a related homologous complex (19, 20) while reverse”
Application of docking methodologies to modeled proteins (2020, methodology): “29 Because of limitations of the experimental techniques, docking often has to rely on the models of proteins instead of the higher-resolution experimentally resolved structures.”
The PPI3D web server for searching, analyzing and modeling protein‐protein interactions in the context of 3D structures (2016, methodology): “Such homology-based analysis may be widely applicable, and a number of software tools exploiting the principle of structural conservation have been developed (Esmaielbeiki et al., 2016; Kawabata, 2016; Szilagyi and Zhang, 2014).”