Marching cubes: A high resolution 3D surface construction algorithm
SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
Thinning Methodologies-A Comprehensive Survey
IEEE Transactions on Pattern Analysis and Machine Intelligence
Improving the Robustness and Accuracy of the Marching Cubes Algorithm for Isosurfacing
IEEE Transactions on Visualization and Computer Graphics
Automatic ultrastructure segmentation of reconstructed CryoEM maps of icosahedral viruses
IEEE Transactions on Image Processing
High-fidelity geometric modeling for biomedical applications
Finite Elements in Analysis and Design
A multiscale model for virus capsid dynamics
Journal of Biomedical Imaging - Special issue on mathematical methods for images and surfaces
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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We present computational solutions to two problemsof macromolecular structure interpretation from reconstructedthree-dimensional electron microscopy (3D-EM) maps of largebio-molecular complexes at intermediate resolution (5A-15A). Thetwo problems addressed are: (a) 3D structural alignment (matching)between identified and segmented 3D maps of structure units(e.g. trimeric configuration of proteins), and (b) the secondarystructure identification of a segmented protein 3D map (i.e.locations of a-helices, b -sheets). For problem (a), we presentan efficient algorithm to correlate spatially (and structurally)two 3D maps of structure units. Besides providing a similarityscore between structure units, the algorithm yields an effectivetechnique for resolution refinement of repeated structure units,by 3D alignment and averaging. For problem (b), we present anefficient algorithm to compute eigenvalues and link eigenvectorsof a Gaussian convoluted structure tensor derived from theprotein 3D Map, thereby identifying and locating secondarystructural motifs of proteins. The efficiency and performanceof our approach is demonstrated on several experimentallyreconstructed 3D maps of virus capsid shells from single-particlecryo-EM, as well as computationally simulated protein structuredensity 3D maps generated from protein model entries in theProtein Data Bank.