Secondary and tertiary structural fold elucidation from 3d EM maps of macromolecules

Authors:
Chandrajit Bajaj;Samrat Goswami
Affiliations:
Department of Computer Sciences, Computational Visualization Center, Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas;Department of Computer Sciences, Computational Visualization Center, Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
Venue:
ICVGIP'06 Proceedings of the 5th Indian conference on Computer Vision, Graphics and Image Processing
Year:
2006

Citing 11
Cited 2

Marching cubes: A high resolution 3D surface construction algorithm

SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
Automatic reconstruction of surfaces and scalar fields from 3D scans

SIGGRAPH '95 Proceedings of the 22nd annual conference on Computer graphics and interactive techniques
Computational geometry: algorithms and applications

Computational geometry: algorithms and applications
NURBS based B-rep models for macromolecules and their properties

SMA '97 Proceedings of the fourth ACM symposium on Solid modeling and applications
The flow complex: a data structure for geometric modeling

SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
A geometric convection approach of 3-D reconstruction

Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing
Shock Graphs and Shape Matching

ICCV '98 Proceedings of the Sixth International Conference on Computer Vision
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes

VIS '04 Proceedings of the conference on Visualization '04
Identifying flat and tubular regions of a shape by unstable manifolds

Proceedings of the 2006 ACM symposium on Solid and physical modeling
Stability and homotopy of a subset of the medial axis

SM '04 Proceedings of the ninth ACM symposium on Solid modeling and applications
Automatic ultrastructure segmentation of reconstructed CryoEM maps of icosahedral viruses

IEEE Transactions on Image Processing

Multi-component heart reconstruction from volumetric imaging

Proceedings of the 2008 ACM symposium on Solid and physical modeling
Describing shapes by geometrical-topological properties of real functions

ACM Computing Surveys (CSUR)

Quantified Score

Hi-index	0.00

Visualization

Abstract

Recent advances in three dimensional Electron Microscopy (3D EM) have given an opportunity to look at the structural building blocks of proteins (and nucleic acids) at varying resolutions. In this paper, we provide algorithms to detect the secondary structural motifs (α-helices and β-sheets) from proteins for which the volumetric maps are reconstructed at 5−10 Å resolution. Additionally, we show that when the resolution is coarser than 10 Å, some of the tertiary structural motifs can be detected from 3D EM. For both these algorithms, we employ the tools from computational geometry and differential topology, specifically the computation of stable/unstable manifolds of certain critical points of the distance function induced by the molecular surface. With the results in this paper, we thus draw a connection between the mathematically well-defined concepts with the bio-chemical structural folds of proteins.