Education

Graduate Student, 08/2001 - present
Bioinformatics and Computational Biology, Iowa State University
B. S., 08/1994
Biochemistry. University of Washington

Previous Research Interests

1. Several lattice models to study protein structure - the fcc and 2-D triangular.  I attempted to prove an upper bound for an energy function for the 2-D case, as well as develop a polynomial time algorithm to solve the HP inverse protein folding problem (IPF).

2. With the fcc model, I investigated several heuristic algorithms to solve the IPF.  I was also interested in using a density parameter, obtained from real proteins, to constrain problems that previously had been shown to be NP-Hard.  With constraints, we may try some new directions.

3.  By using a polynomial time algorithm to solve the IPF problem using a binary amino acid alphabet and real protein coordinates, I examined the relationship between protein sequence and protein structure.  Using a set of globin structures, I generated HP sequences and compared them to the real sequences.  I also did a comparison of the real and generated sequences and found them both to be separated in sequence space.

Current Research Project

We are working with reduced protein models – generally lattice models using a binary amino acid alphabet.  Many studies require an exhaustive search of conformation space within a given rectangle (in 2-D) or parallelepiped (in 3-D).  Using a new method, the transfer matrix method, it is possible to enumerate all conformations contained within a given compact space.  We’re also using this method to examine statistical averages over all conformations, in both compact and non-regular protein shapes.  

 

 

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