Comparing and modeling protein structure. - Rachel Kolodny (2004)

Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons. - Pankaj K. Agarwal; Yonatan Bilu; Rachel Kolodny (WABI, 2005)

Inverse Kinematics in Biology: The Protein Loop Closure Problem. - Rachel Kolodny; Leonidas J. Guibas; Michael Levitt 001; Patrice Koehl (Int. J. Robotics Res., 2005)

VISTAL - a new 2D visualization tool of protein 3D structural alignments. - Rachel Kolodny; Barry Honig (Bioinform., 2006)

Using an alignment of fragment strings for comparing protein structures. - Iddo Friedberg; Tim Harder; Rachel Kolodny; Einat Sitbon; Zhanwen Li; Adam Godzik (Bioinform., 2007)

Redundancy-weighting for better inference of protein structural features. - Chen Yanover; Natalia Vanetik; Michael Levitt 001; Rachel Kolodny; Chen Keasar (Bioinform., 2014)

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations. - Aya Narunsky; Haim Ashkenazy; Rachel Kolodny; Nir Ben-Tal (BMC Bioinform., 2015)

Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich. - Liam M. Longo; Rachel Kolodny; Shawn E. McGlynn (PLoS Comput. Biol., 2022)