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.
|
|
|
