CAD‐score: A new contact area difference‐based function for evaluation of protein structural models

By Kliment Olechnovic, Eleonora Kulberkytė, Č. Venclovas. 2013

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Subfields: Biomedical Engineering, Molecular Biology

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Citations in the corpus

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “To overcome some of the limitations of RMSD in the context of CASP, the Global Distance Test (GDT) was introduced in CASP4 (Zemla, 2003; Zemla et al., 2001).”
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information (2014, methodology): “…have 4 days to predict the 3D structure of the target proteins before models are evaluated against the protein structure coordinates released by the PDB using superposition-independent scoring methods such as Contact Area Difference (CAD) score (24) and local Distance Difference Test (lDDT) (25).”
High‐accuracy protein structure prediction in CASP14 (2021, background): “…evaluates how well the all-atom distance map of the target is reproduced by the model 17 ; (3) CADaa, which compares residues' contact surface areas 18 ; (4) Sphere-Grinder (SG), a measure of local environment conservation 19 ; and (5) ASE, the accuracy self-estimate measure that assesses how well…”
Assessment of model accuracy estimations in CASP12 (2017, methodology): “6 Already in CASP11, we expanded the number of reference measures, adding three non-rigid-body based measures — LDDT, 7 CAD, 8 and SphereGrinder 9 to the evaluation tool chest.”
Methods for estimation of model accuracy in CASP12 (2017, methodology): “However, the true advantage of Pcomb-domain can only be seen if the assessment is based on domains or on using superposition independent evaluation measures like lDDT(55) and CAD-score.(54,55) We calculated the per-residue correlation of local predicted S-scores transformed using S-score formula (se”
Assessment of the model refinement category in CASP12 (2017, methodology): “After 100 iterations, the weights converged, resulting in formula: where the weights for Z LDDT and Z CAD were manually excluded from the final score as they were approaching zero and GDT_TS was very strongly correlated with GDT_HA.”
Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10 (2014, background): “The domain structure consists of an N-terminally located and extended b -strand of 5 nm length [ b 1 comprising residues 7–28; see Fig.”