Assessment of CASP7 predictions in the high accuracy template‐based modeling category

By Randy J. Read, Gayatri Chavali. 2007

108 citations recorded by the source corpus.

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

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “The same also holds for other commonly used model quality metrics, i.e. GDT-HA (Global Distance Test High Accuracy score) (58) and TM-score (Template Modelling score) (59) (Supplementary Figure S1).”
Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, background): “…constant (average Spearman correlation coefﬁcient for segment GDT_TS % 50, 36%); they started to increase slowly for GDT_TS values above 50–60 and then very rapidly for GDT_TS > 80 (average Spearman correlation coefﬁcient for segment GDT_TS > 50, 71%), although some deviations have also been…”
Assessment of the protein-structure refinement category in CASP8 (2009, background): “19 So, we followed previous 19,23 and current assessors, 20 who have applied multiple metrics.”
De novo protein structure prediction by dynamic fragment assembly and conformational space annealing (2011, background): “8,45 CSA searches a wide range of conformational space in the early stages of simulation and narrows down the range of conformational search as the simulation progresses.”
Assessment of template based protein structure predictions in CASP10 (2014, methodology): “1,13,29,30 The goal is to encourage CASP predictions on the TBM class of targets towards the same standards used for experimental protein structure determinations, including accurate positions for all heavy (C, N, O, and S) atoms .”
Evaluation of model refinement in CASP13 (2019, methodology): “In assessing the high-accuracy TBM category in CASP7, we introduced a MR score 15 measuring the utility of models for solving X-ray crystal structures by MR 16 using our program Phaser , 17 ), where we also discuss plans to replace the LLG calculations with an approach that will evaluate the same…”
Protein Structure Prediction: Is It Useful? (2009, methodology): “For proteins with close homologous templates, CM can be used, and most predicted structures have a root mean square deviation (RMSD) of 1–2 Å from the experimental structure, which in some cases achieve the accuracy of medium-resolution NMR or low-resolution X-ray structures [4].”
Evaluation of template-based modeling in CASP13 (2019, methodology): “6,7 However, as the field matures the number of groups achieving high scores on any given model is steadily increasing.”