Rachel Kolodny

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Research interests

I am interested in questions in computational molecular biology, in particular, using sophisticated computational techniques for studying protein structure. I work in two different labs: the Levitt lab, which focuses on structural biology, and the Guibas lab, which focuses on computational geometry. A common thread in my studies is trying to quantify, or mathematically model, biological observations. My current research revolves around three projects: the first project offers a particularly efficient approximation for modeling protein structure using backbone fragments; the second project is an in-depth study of protein structure alignment, which includes a proof that the best alignment can be found in polynomial time, and a large scale comparison of structural alignment methods; the third project outlines a fast algorithm for multiple sequence alignment, which relies on conservation of biological sequence patterns.

Recent publications

R. Kolodny and N. Linial (2004), Approximate Protein Structural Alignment in Polynomial Time, Proc. Natl. Acad. Sci. USA, 101 (33) , 12201-12206.   
R. Kolodny, M. Levitt, Protein Decoy Assembly Using Short Fragments Under Geometric Constraints, Biopolymers, 68 (2003), 2780285.   
R. Kolodny, P. Koehl, L. Guibas and M. Levitt, Small Libraries of Protein Fragments Model Native Protein Structures Accurately, J. Mol. Biol. 323(2002) 323, 297-307.