ORCID

0000-0002-8552-5337(Sazzed), 0000-0001-5326-3152 (Wriggers)

College

College of Sciences

Program

Ph.D. Computer Science

Publication Date

Spring 2020

DOI

10.25883/gsfh-vx68

Abstract

Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a range from zero to one, providing a local measure of cylindrical agreement between the density and atomic model of a helix. A systematic scan of 30,994 helices (among 3,247 protein chains modeled into medium-resolution density maps) reveals an actual range of observed F1 scores from 0.171 to 0.848, suggesting that the local similarity is quantified and discriminated as intended. The best (highest) F1 scores tend to be associated with regions that exhibit high and spatially homogeneous local resolution (between 5 Å to 7.5 Å) in the helical density. The proposed F1 scores can be used as a discriminative classifier for validation studies and as a ranking criterion for cryo-EM density features in databases.

Keywords

Cryo-electron microscopy (cryo-EM), Electron Microscopy Data Bank (EMDB), Helix, F1 scores, Resolution, Density maps

Disciplines

Bioinformatics | Structural Biology | Theory and Algorithms

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Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps


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