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Molecular Surface Abstraction

PhD thesis from University of Wisconsin Madison — 2010
Download the publication : gregc-thesis-small.pdf [14.8Mo]  
In every field of scientific inquiry, new tools and techniques are allowing scientists to acquire everincreasing amounts of data. The field of molecular biology is an important example of this trend: not only are many molecules themselves large and complex, but the way in which they interact with their environment may be difficult to understand and describe. The region surrounding a protein, known as the surface of interaction or “functional surface”, can provide valuable insight into its function. Unfortunately, due to the complexity of both their geometry and their surface fields, study of these surfaces can be slow and difficult, and important features may be hard to identify. This dissertation describes tools and techniques that I have created to address these issues, all of which use abstraction as a method for reducing complexity. First, with the help of collaborators in biochemistry, I have created novel abstract visualizations that more effectively convey the gestalt of the surface of large molecules. Second, I have developed new multi-scale surface descriptors, to aid in the discovery of potential binding partners and to better classify proteins of unknown function. The main technical contributions include: a method for abstracting the functional surface of a protein, and an online system for building and displaying these abstractions; a method for describing the curvature and anisotropy of the surface of a triangulated mesh at multiple scales; a functional surface descriptor that combines this geometric information with multi-scale electrochemical features; and a method for using this descriptor to learn and predict ligand binding behavior on new protein surfaces.

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BibTex references

  author       = "Cipriano, Gregory",
  title        = "Molecular Surface Abstraction",
  school       = "University of Wisconsin Madison",
  year         = "2010",
  ee           = "http://pages.cs.wisc.edu/~gregc/Research/gregc-thesis-small.pdf",
  url          = "http://graphics.cs.wisc.edu/Papers/2010/Cip10"

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