Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

By Maria T. Buenavista, Daniel B. Roche, Liam J. McGuffin. 2012

48 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

IntFOLD: an integrated web resource for high performance protein structure and function prediction (2019, methodology): “The IntFOLD5-TS method was newly developed for CASP13 and worked via iterative multi-template based modelling (19) using the target-template alignments from 14 alternative methods (SP3 (31), SPARKS2 (31), HHsearch (32), COMA (33), SPARKSX (34), CNFsearch (35) and the eight alternative threading meth”
Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “Predictions that did not obey this latter relationship were of lower completeness; e.g., side chains or whole loops were missing.”
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information (2014, background): “…cores in the identified template structures and such regions where templates which are not closely related share common structural features, are most likely well modelled in the target, while segments of structural variation in templates typically correlate with errors in the model (30,35).”
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models (2017, methodology): “The method has since undergone a number of updates: ModFOLD4 (17), which makes use of IntFOLD2-TS (20) models, and ModFOLD5, which makes use of IntFOLD3-TS (21) models.”
ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates (2017, methodology): “We have had some success at using quality assessment guided multiple template based modelling to improve upon errors in single template models (19), but this approach requires sequence-structure alignments and template data.”
Accurate template‐based modeling in CASP12 using the IntFOLD4‐TS, ModFOLD6, and ReFOLD methods (2018, methodology): “These MTM approaches were first introduced in our IntFOLD2-TS method and they are fully described and benchmarked in our article published in 2012.(2) The alternative MTM alignment selection methods resulted in the generation of a new population of up to 124 multi-template models for each target.”
The ModFOLD4 server for the quality assessment of 3D protein models (2013, methodology): “The target sequence is then processed via the IntFOLD2 tertiary structure prediction pipeline (IntFOLD2-TS) (18,19).”
The FunFOLD2 server for the prediction of protein–ligand interactions (2013, methodology): “(A) A number of alternative models are built for the target sequence using the IntFOLD2-TS protocol (4).”
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences (2015, background): “elling approach that is guided by global and local quality estimates (3).”