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Rachel Kolodny, Ph.D. - Publications

Affiliations: 
2004 Stanford University, Palo Alto, CA 
Area:
computational structural biology
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Qiu K, Ben-Tal N, Kolodny R. Similar protein segments shared between domains of different evolutionary lineages. Protein Science : a Publication of the Protein Society. 31: e4407. PMID 36040261 DOI: 10.1002/pro.4407  0.354
2022 Ben-Tal N, Kolodny R. Homologues not needed: Structure prediction from a protein language model. Structure (London, England : 1993). 30: 1047-1049. PMID 35931059 DOI: 10.1016/j.str.2022.07.002  0.425
2022 Jackson C, Toth-Petroczy A, Kolodny R, Hollfelder F, Fuxreiter M, Caroline Lynn Kamerlin S, Tokuriki N. Adventures on the routes of protein evolution - in memoriam Dan Salah Tawfik (1955 - 2021). Journal of Molecular Biology. 167462. PMID 35104498 DOI: 10.1016/j.jmb.2022.167462  0.356
2021 Osadchy M, Kolodny R. How Deep Learning Tools Can Help Protein Engineers Find Good Sequences. The Journal of Physical Chemistry. B. PMID 34105961 DOI: 10.1021/acs.jpcb.1c02449  0.323
2021 Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Erratum to: Bridging themes: short protein segments found in different architectures. Molecular Biology and Evolution. PMID 34009324 DOI: 10.1093/molbev/msab097  0.31
2021 Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Bridging themes: short protein segments found in different architectures. Molecular Biology and Evolution. PMID 33502503 DOI: 10.1093/molbev/msab017  0.304
2020 Cohen M, Pignatti E, Dines M, Mory A, Ekhilevitch N, Kolodny R, Flück CE, Tiosano D. In Silico Structural and Biochemical Functional Analysis of a Novel Pathogenic Variant. International Journal of Molecular Sciences. 21. PMID 32824094 DOI: 10.3390/Ijms21165857  0.461
2020 Narunsky A, Kessel A, Solan R, Alva V, Kolodny R, Ben-Tal N. On the evolution of protein-adenine binding. Proceedings of the National Academy of Sciences of the United States of America. PMID 32079721 DOI: 10.1073/Pnas.1911349117  0.429
2019 Narunsky A, Ben-Tal N, Kolodny R. Navigating Among Known Structures in Protein Space. Methods in Molecular Biology (Clifton, N.J.). 1851: 233-249. PMID 30298400 DOI: 10.1007/978-1-4939-8736-8_12  0.579
2019 Narunsky A, Solan R, Kessel A, Kolodny R, Ben-Tal N. Protein Databank Survey Hints into the Emergence of Protein-Adenine Recognition in Evolution Biophysical Journal. 116: 152a. DOI: 10.1016/J.Bpj.2018.11.846  0.497
2018 Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS. Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins. Elife. 7. PMID 30489257 DOI: 10.7554/Elife.40308  0.485
2018 Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG. Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. Structure (London, England : 1993). PMID 30057025 DOI: 10.1016/J.Str.2018.06.007  0.349
2018 Budowski-Tal I, Kolodny R, Mandel-Gutfreund Y. A Novel Geometry-Based Approach to Infer Protein Interface Similarity. Scientific Reports. 8: 8192. PMID 29844500 DOI: 10.1038/S41598-018-26497-Z  0.521
2018 Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS. Author response: Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins Elife. DOI: 10.7554/Elife.40308.028  0.437
2017 Nepomnyachiy S, Ben-Tal N, Kolodny R. Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths. Proceedings of the National Academy of Sciences of the United States of America. 114: 11703-11708. PMID 29078314 DOI: 10.1073/Pnas.1707642114  0.521
2015 Narunsky A, Nepomnyachiy S, Ashkenazy H, Kolodny R, Ben-Tal N. ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure. Structure (London, England : 1993). 23: 2162-70. PMID 26455800 DOI: 10.1016/J.Str.2015.08.018  0.514
2015 Nepomnyachiy S, Ben-Tal N, Kolodny R. CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers. Structure (London, England : 1993). 23: 941-8. PMID 25865247 DOI: 10.1016/J.Str.2015.02.013  0.372
2015 Nepomnyachiy S, Ben-Tal N, Kolodny R. CyToServer -- A developer tool to bridge between network and 3D-structure F1000research. 4. DOI: 10.7490/F1000Research.1110155.1  0.302
2015 Narunsky A, Ashkenazy H, Kolodny R, Ben-Tal N. Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations Bmc Bioinformatics. 16: 1-3. DOI: 10.1186/1471-2105-16-S3-A3  0.511
2015 Nepomnyachiy S, Kolodny R, Ben-Tal N. Navigating in the Protein Universe Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1124  0.489
2014 Nepomnyachiy S, Ben-Tal N, Kolodny R. Global view of the protein universe. Proceedings of the National Academy of Sciences of the United States of America. 111: 11691-6. PMID 25071170 DOI: 10.1073/Pnas.1403395111  0.385
2014 Yanover C, Vanetik N, Levitt M, Kolodny R, Keasar C. Redundancy-weighting for better inference of protein structural features. Bioinformatics (Oxford, England). 30: 2295-301. PMID 24771517 DOI: 10.1093/Bioinformatics/Btu242  0.648
2014 Ben-Tal N, Kolodny R. Representation of the protein universe using classifications, maps, and networks Israel Journal of Chemistry. DOI: 10.1002/Ijch.201400001  0.55
2013 Kolodny R, Pereyaslavets L, Samson AO, Levitt M. On the universe of protein folds. Annual Review of Biophysics. 42: 559-82. PMID 23527781 DOI: 10.1146/Annurev-Biophys-083012-130432  0.644
2013 Kolodny R, Kosloff M. From protein structure to function via computational tools and approaches Israel Journal of Chemistry. 53: 147-156. DOI: 10.1002/Ijch.201200078  0.588
2013 Keasar C, Kolodny R. Using protein fragments for searching and data-mining protein databases Aaai Workshop - Technical Report. 14-19.  0.403
2011 Osadchy M, Kolodny R. Maps of protein structure space reveal a fundamental relationship between protein structure and function. Proceedings of the National Academy of Sciences of the United States of America. 108: 12301-6. PMID 21737750 DOI: 10.1073/Pnas.1102727108  0.522
2011 Gamliel R, Kedem K, Kolodny R, Keasar C. A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers. Bmc Structural Biology. 11: 20. PMID 21542935 DOI: 10.1186/1472-6807-11-20  0.466
2010 Budowski-Tal I, Nov Y, Kolodny R. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. Proceedings of the National Academy of Sciences of the United States of America. 107: 3481-6. PMID 20133727 DOI: 10.1073/Pnas.0914097107  0.564
2008 Kosloff M, Kolodny R. Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins. 71: 891-902. PMID 18004789 DOI: 10.1002/Prot.21770  0.523
2007 Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A. Using an alignment of fragment strings for comparing protein structures Bioinformatics. 23: e219-e224. PMID 17237095 DOI: 10.1093/Bioinformatics/Btl310  0.548
2006 Kolodny R, Honig B. VISTAL--a new 2D visualization tool of protein 3D structural alignments. Bioinformatics (Oxford, England). 22: 2166-7. PMID 16837525 DOI: 10.1093/Bioinformatics/Btl353  0.457
2006 Kolodny R, Petrey D, Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Current Opinion in Structural Biology. 16: 393-8. PMID 16678402 DOI: 10.1016/J.Sbi.2006.04.007  0.583
2005 Kolodny R, Koehl P, Levitt M. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. Journal of Molecular Biology. 346: 1173-88. PMID 15701525 DOI: 10.1016/J.Jmb.2004.12.032  0.62
2005 Kolodny R, Guibas L, Levitt M, Koehl P. Inverse kinematics in biology: The protein loop closure problem International Journal of Robotics Research. 24: 151-163. DOI: 10.1177/0278364905050352  0.635
2004 Kolodny R, Linial N. Approximate protein structural alignment in polynomial time. Proceedings of the National Academy of Sciences of the United States of America. 101: 12201-6. PMID 15304646 DOI: 10.1073/Pnas.0404383101  0.503
2003 Kolodny R, Levitt M. Protein decoy assembly using short fragments under geometric constraints. Biopolymers. 68: 278-85. PMID 12601789 DOI: 10.1002/Bip.10262  0.652
2003 Kolodny R, Koehl P, Guibas L, Levitt M. Corrigendum to “Small Libraries of Protein Fragments Model Native Protein Structures Accurately” Journal of Molecular Biology. 326: 337. DOI: 10.1016/S0022-2836(02)01438-9  0.397
2002 Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. Journal of Molecular Biology. 323: 297-307. PMID 12381322 DOI: 10.1016/S0022-2836(02)00942-7  0.592
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