Templates are available to model nearly all complexes of structurally characterized proteins

By Petras J. Kundrotas, Zhengwei Zhu, Joël Janin, Ilya A. Vakser. 2012

187 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

Improved prediction of protein-protein interactions using AlphaFold2 (2021, background): “Protein docking methodologies refer to how proteins interact and can be divided into two categories; those based on shape complementarity 6 and those based on alignments (both sequence and structure) to structural templates 7 .”
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).”
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment (2019, neutral): “” 10,38,39 In a significant number of cases however, the modeling task remains challenging because the template structure may differ significantly from the structure of the protein to be modeled, or adequate templates cannot be identified.”
TCRmodel: high resolution modeling of T cell receptors from sequence (2018, methodology): “…the predictive performance on this set of benchmark cases using a different restriction on template selection, disallowing any templates from variable domains with 90% or greater sequence identity with the target TCR, in accordance with algorithm benchmarking by the developers of LYRA (26).”
Application of docking methodologies to modeled proteins (2020, background): “25 Consequently, comparative docking has been successful in quaternary structure prediction.”
What Method to Use for Protein-Protein Docking? (2019, background): “While for the set considered here this fraction is 47% (26/55), Kundrotas et al. [34] suggest that it can be substantially higher, although they also note that only about one-third of these templates are of good quality.”
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.”
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, background): “6,7 Challenges for docking algorithms include side chain and backbone conformational changes between unbound and bound structures, large search spaces, and inability to capture key energetic features in grid-based and other rapidly computable functions, leading to false positive models among…”
Template-based structure modeling of protein-protein interactions (2013, methodology): “Template-based docking The third strategy is through structural alignment based recognition and superimposition, also referred to as template-based docking [19 ,20 ,22 ,23,30].”
Limits and potential of combined folding and docking (2021, background): “Template-based modelling works excellently if a complex with significant sequence identity exists in PDB but does not work for novel complexes[21,22].”
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment (2018, background): “” 9,27,28 With the recent progress in both experimental and computational techniques to characterize and model protein assemblies, a closer integration of the different computational approaches for modeling assemblies and their building blocks was called for.”
Protein-protein docking: from interaction to interactome. (2014, unknown): “The systematic study (61) showed that, surprisingly, docking templates are readily available for complexes representing almost all known protein-protein interactions, provided the components themselves have a known structure or can be homology built.”
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment (2016, unknown): “Since the docking or assembly modeling performance may crucially depend on the accuracy of the models of individual subunits, the targets chosen for this experiment were proteins deemed to be readily modeled using templates from the PDB. Interestingly, templates were used mainly to model the structu”
Assessment of ligand binding site predictions in CASP10 (2014, methodology): “34–36 The overall good performances of methods such as Firestar and SP-ALIGN in CASP10, and their ability to identify ligand binding sites in different families of proteins in the absence of close homologue targets indicates that the field of ligand binding site prediction shows a similar trend.”