CASP10 results compared to those of previous CASP experiments

By Andriy Kryshtafovych, Krzysztof Fidelis, John Moult. 2013

105 citations recorded by the source corpus.

We compare results of the community efforts in modeling protein structures in the tenth CASP experiment, with those in earlier CASPs particularly in CASP5, a decade ago. There is a substantial improvement in template based model accuracy as reflected in more successful modeling of regions of structure not easily derived from a single experimental structure template, most likely reflecting intensive work within the modeling community in developing methods that make use of multiple templates, as well as the increased number of experimental structures available. Deriving structural information not obvious from a template is the most demanding as well as one of the most useful tasks that modeling can perform. Thus this is gratifying progress. By contrast, overall backbone accuracy of models appears little changed in the last decade. This puzzling result is explained by two factors—increased database size in some ways makes it harder to choose the best available templates, and the increased intrinsic difficulty of CASP targets as experimental work has progressed to larger and more unusual structures. There is no detectable recent improvement in template‐free modeling, but again, this may reflect the changing nature of CASP targets. Proteins 2014; 82(Suppl 2):164–174. © 2013 Wiley Periodicals, Inc.

Subfields: Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XII (2017, background): “(CASP classifies the difficulty of targets based on sequence and structural similarity to the closest available structural template.(3)) CASP assesses modeling methods in a number of different categories, and these continue to evolve as the field changes.”
Critical Assessment of Methods of Protein Structure Prediction (CASP) – Progress and New directions in Round XI (2016, background): “As noted in previous papers in this series,54,55 in template free (FM) modeling, over the last decade there has been substantial progress in accuracy for small ( 100 residues) targets, building on earlier methodological advances but the techniques used have not appeared to scale to larger…”
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns (2014, methodology): “(a) ROC plot depicting the PPV values for different predictors on the CASP10 dataset.”
Assessment of Refinement of Template-Based Models in CASP11 (2016, methodology): “21 The procedure involves the following steps: (1) calculating the mean and standard deviation of the measure (for example, GDT-HA) for all models 1s (or all predicted structures) of a particular target; (2) calculating the initial Z-scores for the set of models (all model 1s or all predicted struct”
Protein Structure and Function Prediction Using I-TASSER (2015, background): “Signiﬁcant progress has been witnessed in the past two decades in computer-based structure predictions as measured by the community-wide blind CASP experiments (Moult, 2005; Kryshtafovych et al., 2014).”
Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “25 Crystal structures may or may not exactly correspond to the biologically most relevant due to crystal contacts 78 and other peculiarities of the arti ﬁ - cial crystal environment that could have a signi ﬁ cant effect on protein structures.”