Stephanie Zeil’s research while affiliated with Old Dominion University and other places

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Publications (3)


Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix
  • Article

December 2016

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23 Reads

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8 Citations

Journal of Computational Biology: a Journal of Computational Molecular Cell Biology

Stephanie Zeil

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Willy Wriggers

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Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.


An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images

March 2016

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30 Reads

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22 Citations

IEEE/ACM Transactions on Computational Biology and Bioinformatics

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A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to calculate the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, this results in additional computational overhead. We present an efficient method that addresses the secondary structure placement problem dealing with multiple secondary structure predictions and calculates the optimal mapping. The method was tested using 12 simulated images from α-proteins and two Cryo-EM images of α-β proteins. We observed that the rank of the true topologies is consistently improved by using multiple secondary structure predictions instead of the single prediction method. The results show that the algorithm is robust and works well even when errors/misses in the predicted secondary structures are present in the image or the sequence. The results also show that the algorithm is efficient and is able to handle proteins with as many as 33 helices.


Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix

November 2015

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16 Reads

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3 Citations

Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.

Citations (3)


... Dou et al. proposed a flexible fitting of an atomic structure into a cryo-EM map which is guided by the correspondences between α-helices in the atomic model and the cryo-EM map [27]. In the work of [28], a computational method is presented to quantify the agreement between two sets of central axes of α-helices which are relevant to atomic structures and cryo-EM maps. It utilized an arc-length association strategy to characterize the lateral and the longitudinal differences of the two axes. ...

Reference:

Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix
  • Citing Article
  • December 2016

Journal of Computational Biology: a Journal of Computational Molecular Cell Biology

... The number of detected amino acids and 2-way distance are two parameters that have been used previously in accuracy measurement. Length-association method was proposed recently and can be a potentially more sensitive method to evaluate secondary structure detection [45]. ...

Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix
  • Citing Article
  • November 2015

... Most of the graph-based approaches (Al Nasr et al., 2011, 2018Biswas et al., 2017) discussed in Section 1, utilized the cryo-EM skeleton and lengths of the SSEs as extracted features to assign weights to edges of the graph. Due to uncertainty in the cryo-EM image reconstruction, often the density skeleton is not adequately reliable as extracted features. ...

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images
  • Citing Article
  • March 2016

IEEE/ACM Transactions on Computational Biology and Bioinformatics