Rachel Kolodny
Rachel Kolodny
Verified email at cs.haifa.ac.il
Cited by
Cited by
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
R Kolodny, P Koehl, M Levitt
Journal of molecular biology 346 (4), 1173-1188, 2005
Small libraries of protein fragments model native protein structures accurately
R Kolodny, P Koehl, L Guibas, M Levitt
Journal of molecular biology 323 (2), 297-307, 2002
Protein structure comparison: implications for the nature of ‘fold space’, and structure and function prediction
R Kolodny, D Petrey, B Honig
Current opinion in structural biology 16 (3), 393-398, 2006
Approximate protein structural alignment in polynomial time
R Kolodny, N Linial
Proceedings of the National Academy of Sciences 101 (33), 12201-12206, 2004
Sequence‐similar, structure‐dissimilar protein pairs in the PDB
M Kosloff, R Kolodny
Proteins: Structure, Function, and Bioinformatics 71 (2), 891-902, 2008
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately
I Budowski-Tal, Y Nov, R Kolodny
Proceedings of the National Academy of Sciences 107 (8), 3481-3486, 2010
Inverse kinematics in biology: the protein loop closure problem
R Kolodny, L Guibas, M Levitt, P Koehl
The International Journal of Robotics Research 24 (2-3), 151-163, 2005
On the universe of protein folds
R Kolodny, L Pereyaslavets, AO Samson, M Levitt
Annual review of biophysics 42, 559-582, 2013
Maps of protein structure space reveal a fundamental relationship between protein structure and function
M Osadchy, R Kolodny
Proceedings of the National Academy of Sciences 108 (30), 12301-12306, 2011
Using an alignment of fragment strings for comparing protein structures
I Friedberg, T Harder, R Kolodny, E Sitbon, Z Li, A Godzik
Bioinformatics 23 (2), e219-e224, 2007
Global view of the protein universe
S Nepomnyachiy, N Ben-Tal, R Kolodny
Proceedings of the National Academy of Sciences 111 (32), 11691-11696, 2014
Protein decoy assembly using short fragments under geometric constraints
R Kolodny, M Levitt
Biopolymers: Original Research on Biomolecules 68 (3), 278-285, 2003
Potential Antigenic Cross-reactivity Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Dengue Viruses
Y Lustig, S Keler, R Kolodny, N Ben-Tal, D Atias-Varon, E Shlush, ...
Clinical Infectious Diseases, 2020
Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths
S Nepomnyachiy, N Ben-Tal, R Kolodny
Proceedings of the National Academy of Sciences 114 (44), 11703-11708, 2017
Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons
Y Bilu, PK Agarwal, R Kolodny
IEEE/ACM Transactions on Computational Biology and Bioinformatics 3 (4), 408-422, 2006
CyToStruct: augmenting the network visualization of cytoscape with the power of molecular viewers
S Nepomnyachiy, N Ben-Tal, R Kolodny
Structure 23 (5), 941-948, 2015
Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins
MW Franklin, S Nepomnyachyi, R Feehan, N Ben-Tal, R Kolodny, ...
Elife 7, e40308, 2018
Representation of the protein universe using classifications, maps, and networks
N Ben‐Tal, R Kolodny
Israel Journal of Chemistry 54 (8‐9), 1286-1292, 2014
Efflux pumps represent possible evolutionary convergence onto the β-Barrel fold
MW Franklin, S Nepomnyachiy, R Feehan, N Ben-Tal, R Kolodny, ...
Structure 26 (9), 1266-1274. e2, 2018
ConTemplate suggests possible alternative conformations for a query protein of known structure
A Narunsky, S Nepomnyachiy, H Ashkenazy, R Kolodny, N Ben-Tal
Structure 23 (11), 2162-2170, 2015
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