CASP3 comparative modeling evaluation

By T. Jones, Gerard J. Kleywegt. 1999

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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): “In the course of the CASP experiment, model comparison techniques have evolved to reflect the current state of the art of 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”
Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM (2001, methodology): “However, results from previous Critical Assessment of Techniques for Protein Structure Prediction (CASP) suggested that fully automated prediction procedures are less accurate than approaches using some human intervention.(2,3) Why is this so? Can automated methods be improved to match the added val”
A study of quality measures for protein threading models (2001, methodology): “If the models are quite good one of the simplest measure would be to calculate the rmsd between the model and the correct structure, but other measures have also been proposed [29] and used [ 30 ].”
Modeling of loops in protein structures (2000, background): “The last meeting, CASP3, was held in December of 1998 ~Jones & Kleywegt, 1999!. Protein modelers are challenged to model sequences with unknown 3D structure and to submit their predictions to the organizers before the meeting.”
MaxSub: an automated measure for the assessment of protein structure prediction quality (2000, methodology): “For other evaluation methods used in CASP3, we refer the reader to the reports of the homology modeling (Jones and Kleywegt, 1999) and the ab initio (Orengo et al., 1999) assessors, and to the papers of Sippl and colleagues (Sippl et al., 1999) and Venclovas and colleagues (Venclovas et al., 1999).”
3DCoffee: combining protein sequences and structures within multiple sequence alignments. (2004, background): “(a) Each box indicates the average accuracy difference between TC-3D and TCoffee when computing HOM39 MSAs with various structure/sequence ratios: [0–20] (6 values), [21–40] (27 values), [41–60] (44 values), [61–80] (44 values), [81–100] (20 values).”