Assessment of comparative modeling in CASP2
By Andrew C. R. Martin, M. MacArthur, Janet M. Thornton. 1997
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- Marc A. Martí-Renom
- Lorenza Bordoli
- Andriy Kryshtafovych
Citations in the corpus
- lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “…prediction techniques: In the first installments of CASP, root-mean-square deviation (RMSD) between a prediction and the superposed reference structures was used in various forms as the main evaluation criterion (Hubbard, 1999; Jones and Kleywegt, 1999; Martin et al., 1997; Mosimann et al., 1995).”
- RMS/Coverage graphs: A qualitative method for comparing three‐dimensional protein structure predictions (1999, methodology): “The information shown is: (1) prediction ID; (2) predictor group; (3) number of predictions; (4) the number of residues predicted; (5) an RMS; (6) links labeled [p], [i], [s]; (7) the identifier of the PDB chain from which the model is predicted; (8) the SCOP fold code for the PDB code; and (9) the ”
- ESyPred3D: Prediction of proteins 3D structures (2002, background): “Among these critical steps, it is commonly accepted that the target–template alignment step is the most critical (Mosimann et al., 1995; Martin et al., 1997 ).”
- Modeling of loops in protein structures (2000, background): “Loop modeling errors can be approximately deconvoluted into two contributions: ~1! errors in conformation and ~2! errors in orientation of the loop relative to the rest of the protein ~Martin et al., 1997; van Vlijmen & Karplus, 1997!.”
- Automated server predictions in CASP7 (2007, methodology): “78,79 During the following experiments, numerous predictors registered their meth-ods as servers and were assessed separately as part of the CAFASP experiment series.”
- Comparative protein structure modeling of genes and genomes. (2000, background): “The fold of a model can be assessed by a high sequence similarity with the closest template, an energy based Z-score (157, 169), or by conservation of the key functional or structural residues in the target sequence.”