TY - JOUR
T1 - Estimating loop length from CryoEM images at medium resolutions
AU - McKnight, Andrew
AU - Si, Dong
AU - Al Nasr, Kamal
AU - Chernikov, Andrey
AU - Chrisochoides, Nikos
AU - He, Jing
N1 - Funding Information:
Research was funded in part by NSF grants: CCF-1139864, CCF-1136538, and CSI-1136536 and by the Richard T. Cheng Endowment, the ODU MSF fund and the ODU startup fund. Nikos Chrisochoides helped defray publication costs via NSF funding. This article has been published as part of BMC Structural Biology Volume 13 Supplement 1, 2013: Selected articles from the Computational Structural Bioinformatics Workshop 2012. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcstructbiol/ supplements/13/S1.
PY - 2013
Y1 - 2013
N2 - Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2Å. Conclusions: The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as helices, can be detected accurately, and there is a continuous skeleton linking the helices.
AB - Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2Å. Conclusions: The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as helices, can be detected accurately, and there is a continuous skeleton linking the helices.
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U2 - 10.1186/1472-6807-13-S1-S5
DO - 10.1186/1472-6807-13-S1-S5
M3 - Article
C2 - 24565041
AN - SCOPUS:84887414305
SN - 1472-6807
VL - 13
JO - BMC Structural Biology
JF - BMC Structural Biology
IS - SUPPL.1
M1 - S5
ER -