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

Publications (3)

Article
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 betwee...
Article
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 ami...
Article
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 dens...

Citations

... 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. ...
... 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]. ...
... The results indicated that DP-TOSS was superior to Gorgon. Afterwards, Biswas et al. [22] enhanced the performance of DP-TOSS by combining the information from multiple secondary structure prediction servers. They utilized some different structural information, such as the length of secondary structures, the loop length, and the skeleton between two secondary structure traces as a scoring function. ...