Processing and analysis of CASP3 protein structure predictions

By Adam T. Zemla, Č. Venclovas, John Moult, Krzysztof Fidelis. 1999

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Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, neutral): “In contrast to the protein structure prediction field, where there are several widely accepted quality measures; e.g., C α -RMSD, GDT_TS [3], MaxSub [4], TM-score [5], and S-score [6], the IS-score [7] for assessing protein complex models has not achieved wide adoption by the field and the current…”
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13) (2019, methodology): “Domains in which only one method was used have been excluded to make the numbers comparable was solved to high accuracy (GDT_TS 88.4) despite having no alignments, presumably because of its short length and because the design process ensured it had highly typical structure.”
High resolution comparative modeling with RosettaCM (2013, methodology): “We used the structural similarity (as measured by the GDT) between the first models submitted in the CASP10 experiment by the RosettaServer and the state of the art HHpredA (a widely used public server)(Soding et al., 2005) and ZhangServer (the top-performing server in CASP10) as a measure of the ex”
High‐accuracy protein structure prediction in CASP14 (2021, methodology): “For each template, we computed (1) the GDT_HA, (2) the”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, methodology): “We evaluated the model quality of a decoy using the widely used Global Distance Test (GDT; Zemla, 2003; Zemla et al., 1999, 2001), which compares a decoy with its native and generates a quality value between 0 and 100.”
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. (2009, background): “The INF values over base pairing and base stacking (INF all ) and base-pairing interactions alone ( INF bp ). f Global distance test (GDT-TS) values measure the average percentage of atoms within 1, 2, 4, and 8 A ˚ from the target structure (Zemla et al. 1999; Ginalski et al. 2005).”
CASP9 Assessment of Free Modeling Target Predictions (2011, background): “19 GDT measures the global structure quality of a model by counting the percentage of superimposed residues falling within four superposition cutoff distances (1, 2, 4, and 8 A˚) in four different superpositions.”
MEDELLER: homology-based coordinate generation for membrane proteins (2010, methodology): “GDT_TS scores for all the sets that are given in Supplementary Section 2.2.”