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 indepth 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) , 1220112206.



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, 297307.


