Assessment of CASP7 predictions for template‐based modeling targets

By Jürgen Kopp, Lorenza Bordoli, J. Battey, Florian Kiefer, Torsten Schwede. 2007

174 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

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Citations in the corpus

Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, background): “Recent progress measured in the CASP experiments (Kopp et al., 2007; Kryshtafovych et al., 2007) suggests that this coverage is not an unreasonable expectation.”
Evaluation of CASP8 model quality predictions (2009, methodology): “22 We considered a modeled C a atom to be correct, if it falls within 3.8 A˚ of the corresponding experimental position after optimal sequence-dependent LGA alignment.”
CAD‐score: A new contact area difference‐based function for evaluation of protein structural models (2013, background): “Thus, GDT-HA,12 a more stringent version of GDT-TS, uses distance thresholds half the size of those for GDT-TS.”
Atomic-level protein structure refinement using fragment guided molecular dynamics conformation sampling (2011, methodology): “Historically, the GDT-HA score was used as the standard topology measurement for high-resolution protein structure prediction and refinements in CASP experiments (Cozzetto et al., 2009; Keedy et al., 2009; Kopp et al., 2007; MacCallum et al., 2009).”
Assessment of template based protein structure predictions in CASP9 (2011, methodology): “While earlier editions of CASP focused mainly on C a based measures, in CASP7 all-atom measures and checks for physical plausibility were introduced,18,21 and even stronger emphasized in CASP8.”
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12 (2018, unknown): “For completeness, also superposition-dependent measures (such as GDT-HA, TM-score, RMSD or MaxSub) are provided for individual targets.”
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement (2011, methodology): “Recent CASP experiments have witnessed considerable progress in template-based modeling (TBM),1–3 where the efforts have been mainly focused on developing better methods for template identifi-cation4–6 and on combining multiple threading templates to improve the quality of comparative models.”
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 .”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “Typically, models based on a target-template sequence alignment of this degree of similarity, are largely correct (7, 105, 106).”