CASP15 cryo-EM protein and RNA targets: refinement and analysis using experimental maps

By Thomas Mulvaney, Rachael Kretsch, Luc Elliott, J. Beton, Andriy Kryshtafovych, Daniel J. Rigden, Rhiju Das, M. Topf. 2023

13 citations recorded by the source corpus.

CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are only models themselves—their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized density maps to evaluate the predictions by employing a method for ranking the quality of protein chain predictions based on their fit into the experimental density. The fit‐based ranking was found to correlate well with the CASP assessment scores. Overall, the evaluation against the density map indicated that the models are of high accuracy, and occasionally even better than the reference structure in some regions of the model. Local assessment of predicted side chains in a 1.52 Å resolution map showed that side‐chains are sometimes poorly positioned. Additionally, the top 118 predictions associated with 9 protein target reference structures were selected for automated refinement, in addition to the top 40 predictions for 11 RNA targets. For both proteins and RNA, the refinement of CASP15 predictions resulted in structures that are close to the reference target structure. This refinement was successful despite large conformational changes often being required, showing that predictions from CASP‐assessed methods could serve as a good starting point for building atomic models in cryo‐EM maps for both proteins and RNA. Loop modeling continued to pose a challenge for predictors, and together with the lack of consensus amongst models in these regions suggests that modeling, in combination with model‐fit to the density, holds the potential for identifying more flexible regions within the structure.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

  1. Andriy Kryshtafovych
  2. John Moult
  3. Janusz M. Bujnicki
  4. Rhiju Das
  5. Rachael Kretsch
  6. Yang Zhang
  7. Torsten Schwede
  8. Krzysztof Fidelis

In Molecular Biology

  1. Andriy Kryshtafovych
  2. John Moult
  3. Janusz M. Bujnicki
  4. Rhiju Das
  5. Torsten Schwede
  6. Yang Zhang
  7. Rachael Kretsch
  8. E. Andersen

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