BIROn - Birkbeck Institutional Research Online

Scoring functions for cryoEM density fitting

Vasishtan, Daven and Topf, Maya (2011) Scoring functions for cryoEM density fitting. Journal of Structural Biology 174 (2), pp. 333-343. ISSN 1047-8477.

Full text not available from this repository.
Official URL: http://dx.doi.org/10.1016/j.jsb.2011.01.012

Abstract

In fitting atomic structures into cryoEM density maps of macromolecular assemblies, the cross-correlation function (CCF) is the most prevalent method of scoring the goodness-of-fit. However, there are still many possible, less studied ways of scoring fits. In this paper, we introduce four scores new to cryoEM fitting and compare their performance to three known scores. Our benchmark consists of (a) 4 protein assemblies with simulated maps at 5–20 Å resolution, including the heptameric ring of GroEL; and (b) 4 experimental maps of GroEL at not, vert, similar6–23 Å resolution with corresponding fitted atomic models. We perturb each fit 1000 times and assess each new fit with each score. The correlation between a score and the Cα RMSD of each fit from the “correctly” fitted structure shows that the CCF is one of the best scores, but in certain situations could be augmented or even replaced by other scores. For instance, our implementation of a score based on mutual information outperforms or is comparable to the CCF in almost all test cases and our new “envelope score” works as well as the CCF at sub-nanometer resolution but is an order of magnitude faster to calculate. The results also suggest that the width of the Gaussian function used to blur the atomic structure into a density map can significantly affect the fitting process. Finally, we show that our score-testing method, when combined with the Laplacian CCF or the mutual information scores, can be used as a statistical tool for improving cryoEM density fitting.

Item Type: Article
Keyword(s) / Subject(s): Electron cryo-microscopy, density fitting, scoring functions, cross-correlation function, mutual information, Laplacian filtering, envelope score
School or Research Centre: Birkbeck Schools and Research Centres > School of Science > Biological Sciences
Depositing User: Administrator
Date Deposited: 17 Feb 2011 10:55
Last Modified: 17 Apr 2013 12:20
URI: http://eprints.bbk.ac.uk/id/eprint/3075

Archive Staff Only (login required)

Edit/View Item Edit/View Item