Secondary and Tertiary Structural Fold Elucidation from 3D EM Maps of Macromolecules

  • Chandrajit Bajaj
  • Samrat Goswami
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4338)


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.


Saddle Point Protein Data Bank Unstable Manifold Stable Manifold Medial Axis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Chandrajit Bajaj
    • 1
  • Samrat Goswami
    • 1
  1. 1.Department of Computer Sciences, Computational Visualization Center, Institute of Computational Engineering and SciencesUniversity of Texas at AustinAustin

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