Publication Details






Andrew McKnight


Published in Msc Thesis, Computer Science, Old Dominion University, May, 2013




In the post-genomic era, proteomics research presents a new frontier in life sci- ence. Proteins play roles in virtually every biological process, and understanding their atomic structures is the key to unraveling how they carry out their work. Com- pared to the over half million protein sequences in UniProt, only around 25,000 unique sequences have been atomically modeled and deposited to PDB (Protein Databank). Cryoelectron Microscopy (cryoEM) is an important biophysical tech- nique that produces 3D subnanometer resolution images of molecules not amenable to past approaches like x-ray crystallography or nuclear magnetic resonance. De novo modeling is becoming a promising approach to derive the atomic structure of proteins from the cryoEM 3D images at "medium" resolutions{between 5 and 10 A. Distance measurement along 1D skeletons of 3D images is an important step in de novo modeling. Despite the need of such measurement, little has been investigated about its accuracy in searching for an e ective method. We propose a method to re ne the skeletal length via line simpli cation after selecting the appropriate seg- mentation from the density map using Hausdor distances. Complementarily, we developed a motion planning approach to estimate the minimum length of a loop lying completely within a contour of the density map. To test the methods, loops between 1 and 10 residues in length were extracted from atomic structures in PDB and used to generate density maps at 8 A resolution, along with experimentally derived density maps from EMDB (Electron Microscopy Databank).




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