Assessment of homology‐based predictions in CASP5

By Anna Tramontano, V. Morea. 2003

183 citations recorded by the source corpus.

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

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Citations in the corpus

AlphaFold2 and its applications in the fields of biology and medicine (2023, background): “Through this approach, they discovered a small molecule hit compound for CDK20 (Cyclin-dependent Kinase 20) 91 with a Kd value of 8.9 ± 1.6 μ M within 30 days from target selection and after only synthesizing 7 compounds.”
Exploiting evolutionary relationships for predicting protein structures (2003, background): “2) (Tramontano and Morea, 2003).”
Atomic-level protein structure refinement using fragment guided molecular dynamics conformation sampling (2011, background): “Thus, the final structural models are often closer to the template than to the native structure (Tramontano and Morea, 2003).”
The SWISS-MODEL Repository: new features and functionalities (2005, methodology): “Comparative (or homology) modelling has been shown to be the most accurate method (6), able to reliably build 3D protein models with sufﬁcient accuracy for applications such as structure-based drug design, or rational-izing the effects of sequence variations (7–9).”
Assessment of template based protein structure predictions in CASP9 (2011, methodology): “29 The computed Z -scores were used to rank groups according to their overall prediction performance.”
Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, methodology): “Consequently, specific interactions between the ligand TABLE 7: CASPS RESULTS IN THE FUNCTION PREDICTION CATEGORY (FN) Rank CASP ID Name”
Cryo-EM targets in CASP13: overview and evaluation of results (2019, background): “Next, all models that score below the mean (ie, those with negative Zscores) and outliers from the first stage are assigned Zscores of 0, in order not to over-penalize the groups attempting novel strategies.(11) If a group does not submit any predictions on a target, its per-target Zscores are set t”
TASSER: An automated method for the prediction of protein tertiary structures in CASP6 (2005, background): “Second, generating models that are closer to native than the template alignments remains a challenging problem for most structural refinement approaches.(9) Third, for the template-based modeling (including CM and FR), metapredictions,(10,11) which combine”