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\begin{document}

\title{CASP15 cryoEM protein and RNA targets: refinement and analysis using
experimental maps}



\author[1]{Thomas Mulvaney}%
\author[2]{Rachael C. Kretsch}%
\author[3]{Luc Elliott}%
\author[1]{Joe Beton}%
\author[4]{Andriy Kryshtafovych}%
\author[3]{Daniel Rigden}%
\author[2]{Rhiju Das}%
\author[1]{Maya Topf}%
\affil[1]{Leibniz-Institut fur Virologie}%
\affil[2]{Stanford University}%
\affil[3]{University of Liverpool}%
\affil[4]{University of California Davis Genome Center}%


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  \date{May 21, 2024}


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\selectlanguage{english}
\begin{abstract}
CASP assessments primarily rely on comparing predicted coordinates with
experimental reference structures. However, errors in the reference
structures can potentially reduce the accuracy of the assessment. This
issue is particularly prominent in cryoEM-determined structures, and
therefore, in the assessment of CASP15 cryoEM targets, we directly
utilized density maps to evaluate the predictions. A method for ranking
the quality of protein chain predictions based on rigid fitting to
experimental density 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 although local assessment
of predicted side chains in a 1.52 \selectlanguage{ngerman}Å resolution map showed that
side-chains are sometimes poorly positioned. The top 136 predictions
associated with 9 protein target reference structures were selected for
refinement, in addition to the top 40 predictions for 11 RNA targets. To
this end, we have developed an automated hierarchical refinement
pipeline in cryoEM maps. For both proteins and RNA, the refinement of
CASP15 predictions resulted in structures that are close to the
reference target structure, including some regions with better fit to
the density. This refinement was successful despite large conformational
changes and secondary structure element movements often being required,
suggesting that predictions from CASP-assessed methods could serve as a
good starting point for building atomic models in cryoEM maps for both
proteins and RNA. Loop modeling continued to pose a challenge for
predictors with even short loops failing to be accurately modeled or
refined at times. The lack of consensus amongst models suggests that
modeling holds the potential for identifying more flexible regions
within the structure.%
\end{abstract}\selectlanguage{ngerman}%



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\textbf{Hosted file}

\verb`2023.06.21 - Submission CASP15 Cryo-EM Refinement.docx`  available at \url{https://authorea.com/users/631642/articles/650872-casp15-cryoem-protein-and-rna-targets-refinement-and-analysis-using-experimental-maps}

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