Progress over the first decade of CASP experiments

By Andriy Kryshtafovych, Č. Venclovas, Krzysztof Fidelis, John Moult. 2005

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, neutral): “conformations for the correct fold [26,31].”
Outcome of a workshop on archiving structural models of biological macromolecules. (2006, background): “Correspondingly, models can be calculated automatically, although manual intervention can still provide an advantage, especially in more difficult cases (Kryshtafovych et al., 2005).”
Assessment of protein structure refinement in CASP9 (2011, result): “As with the TBM portion of CASP,27 it is very difficult to judge improvement in refinement compared to previ-Figure ous CASPs.”
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison (2010, methodology): “Such model evaluation framework has been very effective in Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments lasting over a decade [28].”
3D Protein Structure Predicted from Sequence (2011, unknown): “, successful search of the vast space of protein conformations for the correct fold [24,29].”
Identification of correct regions in protein models using structural, alignment, and consensus information (2006, unknown): “significantly better than the automatic methods (Kryshtafovych et al. 2005).”
Physics Based Protein Structure Refinement through Multiple Molecular Dynamics Trajectories and Structure Averaging (2013, methodology): “We used different restraints out of the following three choices: (1) weak restraints on all Cas; (2) strong restraints on selected Cas; and (3) a combination of strong restraints on selected regions and weak restraints on the rest.”
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment (2011, unknown): “The average/best GDT-TS values were 73%/80% for D3 and 55%/60% for CXCR4, which is within the range of prediction accuracy observed in CASP for targets of similar difficulty (Kryshtafovych et al., 2005, 2009).”