Publication Details
Andrew McKnight, Dong Si, Kamal Al Nasr, Andrey Chernikov, Nikos Chrisochoides and Jing He.
Published in BMC Structural Biology CSBW Special Issue, doi:10.1186/1472-6807-13-S1-S5, Volume 13, pages S5 -- November, 2013
Abstract
Background Cryoelectron Microscopy (CryoEM) is an important biophysical technique that produces 3-dimensional (3D) images at diff erent resolutions. De novo modeling is becoming a promising approach to derive the atomic structure of proteins from CryoEM 3D images at medium resolutions. Distance measurement along a 1- dimensional (1D) skeleton in the 3D image is an important step in de novo modeling. The points on the skeleton often need to be processed to accurately estimate the distance that corresponds to the loop length. In spite of the need of such measurement, little has been investigated about the accuracy of the measurement in searching for an effective method. Results We have developed a new computational geometric approach to derive a simpli ed 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 0.5A difference of the expected length for 48 of the 50 cases. The test of eighteen experimentally derived CryoEM images shows that twelve cases have error within 2A. Conclusions The tests using both simulated and experimentally derived images show that it is possible for our proposed method to reasonably estimate the loop length along the skeleton if the secondary structure elements, such as -helices, can be detected accurately.
