Cryo-EM targets in CASP13: overview and evaluation of results

By Andriy Kryshtafovych, Sony Malhotra, Bohdan Monastyrskyy, Tristan Cragnolini, Agnel Praveen Joseph, Wah Chiu, Maya Topf. 2019

19 citations recorded by the source corpus.

Structures of seven CASP13 targets were determined using cryo‐electron microscopy (cryo‐EM) technique with resolution between 3.0 and 4.0 Å. We provide an overview of the experimentally derived structures and describe results of the numerical evaluation of the submitted models. The evaluation is carried out by comparing coordinates of models to those of reference structures (CASP‐style evaluation), as well as checking goodness‐of‐fit of modeled structures to the cryo‐EM density maps. The performance of contributing research groups in the CASP‐style evaluation is measured in terms of backbone accuracy, all‐atom local geometry and similarity of inter‐subunit interfaces. The results on the cryo‐EM targets are compared with those on the whole set of eighty CASP13 targets. A posteriori refinement of the best models in their corresponding cryo‐EM density maps resulted in structures that are very close to the reference structure, including some regions with better fit to the density.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

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Citations in the corpus

Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIII (2019, neutral): “These targets tend to be considerably larger than typical in CASP, but once parsed into evaluation domains are less unusual.(3) A fuller account of the procedures used in CASP is available in Reference 4.”
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (2023, methodology): “As per the CASP13 and CASP14 modeling experiments 1,2 , predictions of cryoEM targets were positioned in the density by aligning them to the target and then optimizing local fit to density before refinement using ChimeraX fit-to-map function.”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “A somewhat similar grouping of scoring functions was observed in the CASP13 evaluation of cryo-EM targets, 220 where most scoring functions showed high pairwise correlation (Figure 9b) except EMRinger, which did not correlate well with any other evaluated scoring function.”
CAMEO - Perspectives on the future of fully automated evaluation of structure prediction methods (2021, unknown): “12 The oligomeric lDDT score (oligo-lDDT) is an extension of the lDDT score for protein complexes and has also been used in CASP since CASP13.”