2012
DOI: 10.1073/pnas.1200678109
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Templates are available to model nearly all complexes of structurally characterized proteins

Abstract: Traditional approaches to protein-protein docking sample the binding modes with no regard to similar experimentally determined structures (templates) of protein-protein complexes. Emerging template-based docking approaches utilize such similar complexes to determine the docking predictions. The docking problem assumes the knowledge of the participating proteins' structures. Thus, it provides the possibility of aligning the structures of the proteins and the template complexes. The progress in the development o… Show more

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Cited by 179 publications
(217 citation statements)
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References 33 publications
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“…The analysis protocol we propose relies on sequence data only. As a consequence, our strategy can provide useful information on a protein interface both in remote homology-based complex reconstruction and when no structural template is available, and it is inherently complementary to current methods based on the analysis of structural similarity (42) or sequence similarity (6,7,10,43) to a set of available templates.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…The analysis protocol we propose relies on sequence data only. As a consequence, our strategy can provide useful information on a protein interface both in remote homology-based complex reconstruction and when no structural template is available, and it is inherently complementary to current methods based on the analysis of structural similarity (42) or sequence similarity (6,7,10,43) to a set of available templates.…”
Section: Discussionmentioning
confidence: 99%
“…Similarly to modeling of tertiary structure for single-chain proteins, homology modeling of protein-protein interactions follows a conservation-based approach, in which the quaternary structure of one or more experimentally solved complexes with enough sequence similarity to a target complex (the templates) is projected onto the target. Templatebased techniques have provided models for a large number of protein complexes with structurally solved homologous complexes (7)(8)(9)(10). Unfortunately, proteins involved in homologous protein dimers tend to systematically preserve their interaction mode only for sequence identities above 30-40% (11).…”
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confidence: 99%
“…Homology modeling can be used in generating 3D protein models to compensate this limitation [51,52]. However, high-quality structures are essential for binding pocket detection.…”
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confidence: 99%
“…Among these, a few particular methods deserve praise: the integrative modeling platform [100] and the modeling of complexes based on experimentally determined homologues [101][102][103][104].…”
Section: Predicting From Predictions: Bioinformatics Interface Predicmentioning
confidence: 99%
“…Both methods were benchmarked against ZDOCK and a novel homology-based method (ZTEM) in a recent publication [105]. Kundrotas et al claimed that 'there are enough templates to model nearly all protein complexes' [103] and developed a method to rigidly superimpose the interacting proteins on homologous complexes. Finally, KBDOCK [104] was also recently developed and uses domain-domain homology to model protein complexes.…”
Section: Predicting From Predictions: Bioinformatics Interface Predicmentioning
confidence: 99%