The predicted structure is compared to the true structure from the PDB in terms of lDDT metric34 (link), as this metric reports the domain accuracy without requiring a domain segmentation of chain structures. The distances are either computed between all heavy atoms (lDDT) or only the Cα atoms to measure the backbone accuracy (lDDT-Cα). As lDDT-Cα only focuses on the Cα atoms, it does not include the penalty for structural violations and clashes. Domain accuracies in CASP are reported as GDT33 (link) and the TM-score27 (link) is used as a full chain global superposition metric.
We also report accuracies using the r.m.s.d.95 (Cα r.m.s.d. at 95% coverage). We perform five iterations of (1) a least-squares alignment of the predicted structure and the PDB structure on the currently chosen Cα atoms (using all Cα atoms in the first iteration); (2) selecting the 95% of Cα atoms with the lowest alignment error. The r.m.s.d. of the atoms chosen for the final iterations is the r.m.s.d.95. This metric is more robust to apparent errors that can originate from crystal structure artefacts, although in some cases the removed 5% of residues will contain genuine modelling errors.
We also report accuracies using the r.m.s.d.95 (Cα r.m.s.d. at 95% coverage). We perform five iterations of (1) a least-squares alignment of the predicted structure and the PDB structure on the currently chosen Cα atoms (using all Cα atoms in the first iteration); (2) selecting the 95% of Cα atoms with the lowest alignment error. The r.m.s.d. of the atoms chosen for the final iterations is the r.m.s.d.95. This metric is more robust to apparent errors that can originate from crystal structure artefacts, although in some cases the removed 5% of residues will contain genuine modelling errors.
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