דילוג לתוכן
Systematic structure-based analysis of RET variants in MEN2A and Hirschsprung’s disease, and the paradoxical co-occurrence of both conditions , Bakhman, A. F., Cohen, M., Kolodny, R. & Kosloff, M., Apr 2026 , In: DMM Disease Models and Mechanisms. 19 , 4 , dmm052748.Interpretable prediction of zinc ion location in proteins with ZincSight , Mechtinger, G., Axel, G., Kolodny, R. & Ben-Tal, N., Nov 2025 , In: Protein Science. 34 , 11 , e70350.From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance , Lemay-St-Denis, C., Cellier-Goetghebeur, S., St-Aubin, M., Ide, K., Copp, J. N., Tsuda, S., Ben-Tal, N., Kolodny, R. & Pelletier, J. N., 1 Oct 2025 , In: Molecular Biology and Evolution. 42 , 10 , msaf215.Editorial overview: Sequences and topology (2025) , Elofsson, A. & Kolodny, R., Aug 2025 , In: Current Opinion in Structural Biology. 93 , 103108.A building blocks perspective on protein emergence and evolution , Ezerzer, Y., Frenkel-Pinter, M., Kolodny, R. & Ben-Tal, N., Apr 2025 , In: Current Opinion in Structural Biology. 91 , 102996.Predicting gene sequences with AI to study codon usage patterns , Sidi, T., Bahiri-Elitzur, S., Tuller, T. & Kolodny, R., 7 Jan 2025 , In: Proceedings of the National Academy of Sciences of the United States of America. 122 , 1 , e2410003121.Reused Protein Segments Linked to Functional Dynamics , Kutlu, Y., Axel, G., Kolodny, R., Ben-Tal, N. & Haliloglu, T., 1 Sep 2024 , In: Molecular Biology and Evolution. 41 , 9 , msae184.What can AlphaFold do for antimicrobial amyloids? , Ragonis-Bachar, P., Axel, G., Blau, S., Ben-Tal, N., Kolodny, R. & Landau, M., Feb 2024 , In: Proteins: Structure, Function and Bioinformatics. 92 , 2 , p. 265-281 17 p. Similar protein segments shared between domains of different evolutionary lineages , Qiu, K., Ben-Tal, N. & Kolodny, R., Sep 2022 , In: Protein Science. 31 , 9 , e4407.Homologues not needed: Structure prediction from a protein language model , Ben-Tal, N. & Kolodny, R., 4 Aug 2022 , In: Structure. 30 , 8 , p. 1047-1049 3 p. Adventures on the Routes of Protein Evolution—In Memoriam Dan Salah Tawfik (1955–2021) , Jackson, C., Toth-Petroczy, A., Kolodny, R., Hollfelder, F., Fuxreiter, M., Kamerlin, S. C. L. & Tokuriki, N., 15 Apr 2022 , In: Journal of Molecular Biology. 434 , 7 , 167462.Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich , Longo, L. M., Kolodny, R. & McGlynn, S. E., Feb 2022 , In: PLOS Computational Biology. 18 , 2 , e1009833.Potential Antigenic Cross-reactivity Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Dengue Viruses , Lustig, Y., Keler, S., Kolodny, R., Ben-Tal, N., Atias-Varon, D., Shlush, E., Gerlic, M., Munitz, A., Doolman, R., Asraf, K., Shlush, L. I. & Vivante, A., 1 Oct 2021 , In: Clinical Infectious Diseases. 73 , 7 , p. E2444-E2449 Gram-negative outer-membrane proteins with multiple β-barrel domains , Solan, R., Pereira, J., Lupas, A. N., Kolodny, R. & Ben-Tal, N., 3 Aug 2021 , In: Proceedings of the National Academy of Sciences of the United States of America. 118 , 31 , e2104059118.How Deep Learning Tools Can Help Protein Engineers Find Good Sequences , Osadchy, M. & Kolodny, R., 24 Jun 2021 , In: Journal of Physical Chemistry B. 125 , 24 , p. 6440-6450 11 p. Searching protein space for ancient sub-domain segments , Kolodny, R., Jun 2021 , In: Current Opinion in Structural Biology. 68 , p. 105-112 8 p. Bridging Themes: Short Protein Segments Found in Different Architectures , Kolodny, R., Nepomnyachiy, S., Tawfik, D. S. & Ben-Tal, N., 1 Jun 2021 , In: Molecular Biology and Evolution. 38 , 6 , p. 2191-2208 18 p. On the emergence of p-loop ntpase and rossmann enzymes from a beta-alpha-beta ancestral fragment , Longo, L. M., Jabtoiiska, J., Vyas, P., Kanade, M., Kolodny, R., Ben-Tal, N. & Tawfik, D. S., Dec 2020 , In: eLife. 9 , p. 1-16 16 p. , e64415.In silico structural and biochemical functional analysis of a novel cyp21a2 pathogenic variant , Cohen, M., Pignatti, E., Dines, M., Mory, A., Ekhilevitch, N., Kolodny, R., Flück, C. E. & Tiosano, D., 2 Aug 2020 , In: International Journal of Molecular Sciences. 21 , 16 , p. 1-11 11 p. , 5857.On the evolution of protein-adenine binding , Narunsky, A., Kessel, A., Solan, R., Alva, V., Kolodny, R. & Ben-Tal, N., 3 Mar 2020 , In: Proceedings of the National Academy of Sciences of the United States of America. 117 , 9 , p. 4701-4709 9 p. Navigating Among Known Structures in Protein Space , Narunsky, A., Ben-Tal, N. & Kolodny, R., 2019 , Methods in Molecular Biology. Humana Press Inc., p. 233-249 17 p. (Methods in Molecular Biology; vol. 1851).A novel geometry-based approach to infer protein interface similarity , Budowski-Tal, I., Kolodny, R. & Mandel-Gutfreund, Y., 1 Dec 2018 , In: Scientific Reports. 8 , 1 , 8192.Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins , Franklin, M. W., Nepomnyachyi, S., Feehan, R., Ben-Tal, N., Kolodny, R. & Slusky, J. S. G., 1 Nov 2018 , In: eLife. 7 , e40308.Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold , Franklin, M. W., Nepomnyachiy, S., Feehan, R., Ben-Tal, N., Kolodny, R. & Slusky, J. S. G., 4 Sep 2018 , In: Structure. 26 , 9 , p. 1266-1274.e2 Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths , Nepomnyachiy, S., Ben-Tal, N. & Kolodny, R., 31 Oct 2017 , In: Proceedings of the National Academy of Sciences of the United States of America. 114 , 44 , p. 11703-11708 6 p. Similarity between the Usher Plug and the Repeating Domain of an Ice-adhesin: Evolution via Surface Reshaping , Kessel, A., Kolodny, R. & Ben-Tal, N., 1 May 2017 , In: Israel Journal of Chemistry. 57 , 5 , p. 381-384 4 p. ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure , Narunsky, A., Nepomnyachiy, S., Ashkenazy, H., Kolodny, R. & Ben-Tal, N., 3 Nov 2015 , In: Structure. 23 , 11 , p. 2162-2170 9 p. CyToStruct: Augmenting the network visualization of CyToStruct with the power of molecular viewers , Nepomnyachiy, S., Ben-Tal, N. & Kolodny, R., 5 May 2015 , In: Structure. 23 , 5 , p. 941-948 8 p. Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations , Narunsky, A., Ashkenazy, H., Kolodny, R. & Ben-Tal, N., 2015 , In: BMC Bioinformatics. 16 , S3 Redundancy-weighting for better inference of protein structural features , Yanover, C., Vanetik, N., Levitt, M., Kolodny, R. & Keasar, C., 15 Aug 2014 , In: Bioinformatics. 30 , 16 , p. 2295-2301 7 p. Global view of the protein universe , Nepomnyachiy, S., Ben-Tal, N. & Kolodny, R., 12 Aug 2014 , In: Proceedings of the National Academy of Sciences of the United States of America. 111 , 32 , p. 11691-11696 6 p. Representation of the Protein Universe using Classifications, Maps, and Networks , Ben-Tal, N. & Kolodny, R., 2014 , In: Israel Journal of Chemistry. 54 , 8-9 , p. 1286-1292 7 p. On the universe of protein folds , Kolodny, R., Pereyaslavets, L., Samson, A. O. & Levitt, M., May 2013 , In: Annual Review of Biophysics. 42 , 1 , p. 559-582 24 p. From protein structure to function via computational tools and approaches , Kolodny, R. & Kosloff, M., Apr 2013 , In: Israel Journal of Chemistry. 53 , 3-4 , p. 147-156 10 p. Using protein fragments for searching and data-mining protein databases , Keasar, C. & Kolodny, R., 2013 , Artificial Intelligence and Robotics Methods in Computational Biology - Papers from the 2013 AAAI Workshop, Technical Report. AI Access Foundation, p. 14-19 6 p. (AAAI Workshop - Technical Report; vol. WS-13-06).Maps of protein structure space reveal a fundamental relationship between protein structure and function , Osadchy, M. & Kolodny, R., 26 Jul 2011 , In: Proceedings of the National Academy of Sciences of the United States of America. 108 , 30 , p. 12301-12306 6 p. A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers , Gamliel, R., Kedem, K., Kolodny, R. & Keasar, C., 2011 , In: BMC Structural Biology. 11 , 20.FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately , Budowski-Tal, I., Nov, Y. & Kolodny, R., 23 Feb 2010 , In: Proceedings of the National Academy of Sciences of the United States of America. 107 , 8 , p. 3481-3486 6 p. A new library of surface patches - design and applications , Gamliel, R., Kedem, K., Kolodny, T. R. & Keasar, C., 2009 , Ben-Gurion University. 33 p. Sequence-similar, structure-dissimilar protein pairs in the PDB , Kosloff, M. & Kolodny, R., 1 May 2008 , In: Proteins: Structure, Function and Genetics. 71 , 2 , p. 891-902 12 p. Using an alignment of fragment strings for comparing protein structures , Friedberg, I., Harder, T., Kolodny, R., Sitbon, E., Li, Z. & Godzik, A., 2007 , In: Bioinformatics. 23 , 2 , p. e219-e224 Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons , Bilu, Y., Agarwal, P. K. & Kolodny, R., Oct 2006 , In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 3 , 4 , p. 408-422 15 p. VISTAL - A new 2D visualization tool of protein 3D structural alignments , Kolodny, R. & Honig, B., 1 Sep 2006 , In: Bioinformatics. 22 , 17 , p. 2166-2167 2 p. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction , Kolodny, R., Petrey, D. & Honig, B., Jun 2006 , In: Current Opinion in Structural Biology. 16 , 3 , p. 393-398 6 p. Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures , Kolodny, R., Koehl, P. & Levitt, M., 4 Mar 2005 , In: Journal of Molecular Biology. 346 , 4 , p. 1173-1188 16 p. Inverse kinematics in biology: The protein loop closure problem , Kolodny, R., Guibas, L., Levitt, M. & Koehl, P., Feb 2005 , In: International Journal of Robotics Research. 24 , 2-3 , p. 151-163 13 p. Faster algorithms for optimal Multiple Sequence Alignment based on pairwise comparisons , Agarwal, P. K., Bilu, Y. & Kolodny, R., 2005 , Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). p. 315-327 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3692 LNBI).Approximate protein structural alignment in polynomial time , Kolodny, R. & Linial, N., 17 Aug 2004 , In: Proceedings of the National Academy of Sciences of the United States of America. 101 , 33 , p. 12201-12206 6 p. Protein decoy assembly using short fragments under geometric constraints , Kolodny, R. & Levitt, M., Mar 2003 , In: Biopolymers. 68 , 3 , p. 278-285 8 p. Small libraries of protein fragments model native protein structures accurately , Kolodny, R., Koehl, P., Guibas, L. & Levitt, M., 2002 , In: Journal of Molecular Biology. 323 , 2 , p. 297-307 11 p.
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