Evaluation of template-based models in CASP8 with standard measures

By Domenico Cozzetto, Andriy Kryshtafovych, Krzysztof Fidelis, John Moult, Burkhard Rost, Anna Tramontano. 2009

154 citations recorded by the source corpus.

The strategy for evaluating template‐based models submitted to CASP has continuously evolved from CASP1 to CASP5, leading to a standard procedure that has been used in all subsequent editions. The established approach includes methods for calculating the quality of each individual model, for assigning scores based on the distribution of the results for each target and for computing the statistical significance of the differences in scores between prediction methods. These data are made available to the assessor of the template‐based modeling category, who uses them as a starting point for further evaluations and analyses. This article describes the detailed workflow of the procedure, provides justifications for a number of choices that are customarily made for CASP data evaluation, and reports the results of the analysis of template‐based predictions at CASP8. Proteins 2009. © 2009 Wiley‐Liss, Inc.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

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Citations in the corpus

PROTEIN STRUCTURE PREDICTION CENTER IN CASP8 (2009, methodology): “According to the recommendations of the CASP7 Predictors’ Meeting, the selected target sequences were split into two categories: (1) targets for prediction by all groups (human/server targets) and (2) targets for server prediction (server-only targets).”
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment (2011, unknown): “Target difficulty was evaluated using standard CASP measures (Cozzetto et al., 2009) and the LGA (Local-Global Alignment) package (Zemla, 2003) kindly provided by Dr. Adam Zemla.”
Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe (2010, background): “In comparison, there are over 1.4 million known organisms (Leipe, 1996) while estimates of the total number of species on earth vary between 4 and 100 million (Crandall and Buhay, 2004).”
Atomic-level protein structure refinement using fragment guided molecular dynamics conformation sampling (2011, methodology): “Historically, the GDT-HA score was used as the standard topology measurement for high-resolution protein structure prediction and refinements in CASP experiments (Cozzetto et al., 2009; Keedy et al., 2009; Kopp et al., 2007; MacCallum et al., 2009).”
I-TASSER: a unified platform for automated protein structure and function prediction (2010, methodology): “is one example of the composite approaches and has been ranked as the best method for the automated protein structure prediction in the last two CASP experiment”
CASP PREDICTION CENTER INFRASTRUCTURE AND EVALUATION MEASURES IN CASP10 AND CASP ROLL (2013, background): “The CASP system allows registration of participants for both experiments in one of the following roles: (1) an expert group leader; (2) a server group leader; (3) a member of a prediction group; or (4) an observer.”
Assessment of template based protein structure predictions in CASP9 (2011, background): “19,20 In the template based modeling category, all models can be expected to be physically realistic and plausible.”
Computational Methods in Drug Discovery (2014, background): “model that deviate from corresponding residues in the target by no more than a specified distance, whereas AL0 represents the percentage of correctly aligned residues (Cozzetto et al., 2009).”
CAD‐score: A new contact area difference‐based function for evaluation of protein structural models (2013, background): “8 However, despite its common use, GDT-based scoring is not without weaknesses.”
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement (2011, methodology): “The I-TASSER force field includes four components: (1) general knowledge-based statistical terms from the PDB (Ca/side-chain correlations,37 hydrogen-bond,38 and hydrophobicity39); (2) spatial restraints collected from threading templates7; (3) sequence-based Ca/Cb/sidechain center contact predictio”