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           COLLOQUIUM OF THE COMPUTATIONAL MATERIALS SCIENCE CENTER
                              College of Science
                       (CDS Department CSI 898-Sec 001)
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     Analysis of Inter-residue Contact Patterns in Delaunay 
                 Tessellated Protein Structures.

                        Todd Taylor
 National Institute of Standards and Technology, Gaithersburg, MD

Delaunay tessellation, a technique from computational geometry for 
uniquely decomposing a point set into non-overlapping tetrahedral 
subsets, has proven extremely versatile in the analysis of protein 
structures. This talk will detail results from a few applications 
where we largely ignore amino acid identities and restrict our 
attention to the pattern of contacts between residues.

I will describe a definition of protein secondary structure that, 
unlike existing methods,  uses only patterns of carbon alpha contacts 
and has no explicit dependence on angles, lengths, or areas. It uses 
structural descriptors called t-numbers, defined in terms of the 
Delaunay tessellation, and agrees very well with more conventional 
definitions based on putative hydrogen-bonding patterns.

I will discuss a  simple method of protein structural domain 
decomposition based on the Potts model from statistical physics. 
Each residue in a tessellated protein is considered a site in an 
irregular lattice where lattice neighbors are joined by Delaunay 
edges. Integer value 'spins' are assigned to each residue/site, and 
they interact via a simple Ising/Potts ferromagnetic-like energy 
function. Clusters of like spins emerge as if they were magnetic 
domains and the clusters correspond closely to human expert assigned 
protein structural domains.

Finally, I will talk about some properties of protein inter-residue 
Delaunay contact graphs (scaling properties, effective dimensionality)  
and compare them to properties of contact graphs from some simple, 
computationally derived sets of model structures. 

                        Monday, April 28, 2008
                                  4:30 pm
                     Room 301, Research I, Fairfax Campus

Refreshments will be served at 4:15 PM.
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Find the schedule at www.cmasc.gmu.edu/seminar/schedule.html
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