| Year |
Citation |
Score |
| 2023 |
Girodat D, Wieden HJ, Blanchard SC, Sanbonmatsu KY. Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding. Nature Communications. 14: 5582. PMID 37696823 DOI: 10.1038/s41467-023-40404-9 |
0.797 |
|
| 2022 |
Prajapati JD, Onuchic JN, Sanbonmatsu KY. Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts. Journal of Molecular Biology. 167788. PMID 35963460 DOI: 10.1016/j.jmb.2022.167788 |
0.629 |
|
| 2022 |
Nishima W, Girodat D, Holm M, Rundlet EJ, Alejo JL, Fischer K, Blanchard SC, Sanbonmatsu KY. Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting. Nucleic Acids Research. PMID 35808938 DOI: 10.1093/nar/gkac597 |
0.804 |
|
| 2022 |
Miner JC, Fenimore PW, Fischer WM, McMahon BH, Sanbonmatsu KY, Tung CS. Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022). Current Research in Structural Biology. 4: 220-230. PMID 35765663 DOI: 10.1016/j.crstbi.2022.06.004 |
0.307 |
|
| 2022 |
Sanbonmatsu K. Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. Advances in Experimental Medicine and Biology. 1363: 23-32. PMID 35220564 DOI: 10.1007/978-3-030-92034-0_3 |
0.44 |
|
| 2021 |
Lappala A, Wang CY, Kriz A, Michalk H, Tan K, Lee JT, Sanbonmatsu KY. Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34645712 DOI: 10.1073/pnas.2107092118 |
0.758 |
|
| 2021 |
Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 34642784 DOI: 10.1007/s00335-021-09924-x |
0.443 |
|
| 2021 |
Sarkar R, Jaiswar A, Hennelly SP, Onuchic JN, Sanbonmatsu KY, Roy S. Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation. The Journal of Physical Chemistry. B. PMID 34106719 DOI: 10.1021/acs.jpcb.1c02467 |
0.806 |
|
| 2021 |
Miner JC, Lappala A, Fenimore PW, Fischer WM, McMahon BH, Hengartner NW, Sanbonmatsu KY, Tung CS. Modeling the NP-vRNA-Polymerase Complex in Atomic Detail. Biomolecules. 11. PMID 33477938 DOI: 10.3390/biom11010124 |
0.792 |
|
| 2020 |
Girodat D, Pati AK, Terry DS, Blanchard SC, Sanbonmatsu KY. Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein. Plos Computational Biology. 16: e1008293. PMID 33151943 DOI: 10.1371/journal.pcbi.1008293 |
0.804 |
|
| 2020 |
Kim DN, Gront D, Sanbonmatsu KY. Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. Journal of Chemical Information and Modeling. PMID 32422044 DOI: 10.1021/Acs.Jcim.0C00090 |
0.712 |
|
| 2020 |
Girodat D, Blanchard SC, Wieden HJ, Sanbonmatsu KY. Elongation Factor-Tu switch I is a gate for aminoacyl-tRNA selection. Journal of Molecular Biology. PMID 32061931 DOI: 10.1016/J.Jmb.2020.01.038 |
0.794 |
|
| 2020 |
Morse JC, Girodat D, Burnett BJ, Holm M, Altman RB, Sanbonmatsu KY, Wieden HJ, Blanchard SC. Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection. Proceedings of the National Academy of Sciences of the United States of America. PMID 32024753 DOI: 10.1073/Pnas.1904469117 |
0.8 |
|
| 2020 |
Kim DN, Thiel BC, Mrozowich T, Hennelly SP, Hofacker IL, Patel TR, Sanbonmatsu KY. Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nature Communications. 11: 148. PMID 31919376 DOI: 10.1038/S41467-019-13942-4 |
0.824 |
|
| 2020 |
Sanbonmatsu KY. Going Big: Million Atom Simulations of Ribosomes and Billion Atom Simulations of Chromatin Biophysical Journal. 118: 352a. DOI: 10.1016/J.Bpj.2019.11.2032 |
0.403 |
|
| 2019 |
Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K. cryo_fit: Democratization of Flexible Fitting for Cryo-EM. Journal of Structural Biology. PMID 31279069 DOI: 10.1016/J.Jsb.2019.05.012 |
0.795 |
|
| 2019 |
Sanbonmatsu KY. Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR. Current Opinion in Structural Biology. 55: 104-113. PMID 31125796 DOI: 10.1016/J.Sbi.2019.03.004 |
0.479 |
|
| 2019 |
Jung J, Nishima W, Daniels M, Bascom G, Kobayashi C, Adedoyin A, Wall M, Lappala A, Phillips D, Fischer W, Tung CS, Schlick T, Sugita Y, Sanbonmatsu KY. Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations. Journal of Computational Chemistry. PMID 30994934 DOI: 10.1002/Jcc.25840 |
0.762 |
|
| 2019 |
Sanbonmatsu KY. Stalking Structure in Plant Long Noncoding RNAs. Methods in Molecular Biology (Clifton, N.J.). 1933: 381-388. PMID 30945198 DOI: 10.1007/978-1-4939-9045-0_23 |
0.478 |
|
| 2019 |
Roy S, Hennelly SP, Lammert H, Onuchic JN, Sanbonmatsu KY. Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch. Nucleic Acids Research. PMID 30605518 DOI: 10.1093/Nar/Gky1311 |
0.778 |
|
| 2018 |
Yang F, Kunde YA, Hennelly SP, Sanbonmatsu KY, Starkenburg SR, Goodwin PM. High-throughput Mapping of Cotranscriptional Assembly of the 30S Ribosomal Subunit Biophysical Journal. 114: 64a. DOI: 10.1016/J.Bpj.2017.11.398 |
0.363 |
|
| 2018 |
Nishima W, Blanchard SC, Sanbonmatsu KY. Exaggerated Swivel Motions of the Small Subunit Head Domain are Required for tRNA Translocation through the Bacterial Ribosome Biophysical Journal. 114: 437a. DOI: 10.1016/J.Bpj.2017.11.2419 |
0.386 |
|
| 2017 |
Kim DN, Sanbonmatsu K. Tools for the Cryo-EM Gold Rush: Going from the cryo-EM map to the atomistic model. Bioscience Reports. PMID 28963369 DOI: 10.1042/Bsr20170072 |
0.703 |
|
| 2017 |
Liu W, Shin D, Ng M, Sanbonmatsu KY, Tor Y, Cooperman BS. Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position. Molecules (Basel, Switzerland). 22. PMID 28850078 DOI: 10.3390/Molecules22091427 |
0.594 |
|
| 2017 |
Roy S, Onuchic JN, Sanbonmatsu KY. Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch. Biophysical Journal. 113: 348-359. PMID 28746845 DOI: 10.1016/J.Bpj.2017.06.044 |
0.631 |
|
| 2017 |
Zhang B, Mao YS, Diermeier SD, Novikova IV, Nawrocki EP, Jones TA, Lazar Z, Tung CS, Luo W, Eddy SR, Sanbonmatsu KY, Spector DL. Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Reports. 19: 1723-1738. PMID 28538188 DOI: 10.1016/J.Celrep.2017.05.006 |
0.758 |
|
| 2017 |
Gulay SP, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu KY, Dinman JD. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Research. PMID 28334755 DOI: 10.1093/Nar/Gkx112 |
0.788 |
|
| 2017 |
Roy S, Lammert H, Hayes RL, Chen B, LeBlanc R, Dayie TK, Onuchic JN, Sanbonmatsu KY. A magnesium-induced triplex pre-organizes the SAM-II riboswitch. Plos Computational Biology. 13: e1005406. PMID 28248966 DOI: 10.1371/Journal.Pcbi.1005406 |
0.58 |
|
| 2017 |
Sanbonmatsu KY, Nishima W. Simulating Movement of the Ribosome Head during Translocation Biophysical Journal. 112: 68a. DOI: 10.1016/J.Bpj.2016.11.407 |
0.423 |
|
| 2016 |
Li N, Hennelly SP, Stubben CJ, Micheva-Viteva S, Hu B, Shou Y, Vuyisich M, Tung CS, Chain PS, Sanbonmatsu KY, Hong-Geller E. Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages. Plos One. 11: e0168915. PMID 28030576 DOI: 10.1371/Journal.Pone.0168915 |
0.789 |
|
| 2016 |
Hawkes EJ, Hennelly SP, Novikova IV, Irwin JA, Dean C, Sanbonmatsu KY. COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. Cell Reports. 16: 3087-96. PMID 27653675 DOI: 10.1016/J.Celrep.2016.08.045 |
0.812 |
|
| 2016 |
Xue Z, Hennelly S, Doyle B, Gulati AA, Novikova IV, Sanbonmatsu KY, Boyer LA. A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Molecular Cell. PMID 27618485 DOI: 10.1016/J.Molcel.2016.08.010 |
0.818 |
|
| 2016 |
Bascom GD, Sanbonmatsu KY, Schlick T. Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. The Journal of Physical Chemistry. B. PMID 27218881 DOI: 10.1021/Acs.Jpcb.6B03197 |
0.402 |
|
| 2016 |
Sanbonmatsu KY. Towards structural classification of long non-coding RNAs. Biochimica Et Biophysica Acta. 1859: 41-5. PMID 26537437 DOI: 10.1016/J.Bbagrm.2015.09.011 |
0.515 |
|
| 2015 |
Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Physical Review Letters. 114: 258105. PMID 26197147 DOI: 10.1103/Physrevlett.114.258105 |
0.756 |
|
| 2015 |
Krishnamurthy M, Hennelly SP, Dale T, Starkenburg SR, Martí-Arbona R, Fox DT, Twary SN, Sanbonmatsu KY, Unkefer CJ. Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression. Acs Synthetic Biology. PMID 26165796 DOI: 10.1021/Acssynbio.5B00041 |
0.751 |
|
| 2015 |
Kirmizialtin S, Loerke J, Behrmann E, Spahn CM, Sanbonmatsu KY. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods in Enzymology. 558: 497-514. PMID 26068751 DOI: 10.1016/Bs.Mie.2015.02.011 |
0.721 |
|
| 2015 |
Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods in Enzymology. 553: 215-34. PMID 25726467 DOI: 10.1016/Bs.Mie.2014.10.061 |
0.815 |
|
| 2015 |
Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM. Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES. Molecular Cell. 57: 422-32. PMID 25601755 DOI: 10.1016/J.Molcel.2014.12.016 |
0.47 |
|
| 2015 |
Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CMT. Cryo-Em Structures of Ribosomal 80S Complexes with Termination Factors and Cricket Paralysis Virus Ires Reveal the Ires in the Translocated State Molecular Cell. 57: 422. DOI: 10.2210/Pdb4D5Y/Pdb |
0.394 |
|
| 2015 |
Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere Physical Review Letters. 114. DOI: 10.1103/PhysRevLett.114.258105 |
0.71 |
|
| 2015 |
Kaushal PS, Sharma MR, Booth TM, Haque EM, Tung CS, Sanbonmatsu KY, Spremulli LL, Agrawal RK. Correction: Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 20 (7284-7289) DOI: 10.1073/pnas.1401657111) Proceedings of the National Academy of Sciences of the United States of America. 112: E2736. DOI: 10.1073/Pnas.1507224112 |
0.39 |
|
| 2015 |
Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Magnesium Dependence of the RNA Free Energy Landscape Biophysical Journal. 108: 235a. DOI: 10.1016/J.Bpj.2014.11.1301 |
0.757 |
|
| 2014 |
Sanbonmatsu KY. Flipping through the genetic code: new developments in discrimination between cognate and near-cognate tRNAs and the effect of antibiotics. Journal of Molecular Biology. 426: 3197-200. PMID 25017628 DOI: 10.1016/J.Jmb.2014.07.005 |
0.345 |
|
| 2014 |
Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM. Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell. 158: 121-31. PMID 24995983 DOI: 10.1016/J.Cell.2014.04.044 |
0.448 |
|
| 2014 |
Sanbonmatsu KY. Dynamics of riboswitches: Molecular simulations. Biochimica Et Biophysica Acta. 1839: 1046-1050. PMID 24953187 DOI: 10.1016/J.Bbagrm.2014.06.010 |
0.487 |
|
| 2014 |
Kaushal PS, Sharma MR, Booth TM, Haque EM, Tung CS, Sanbonmatsu KY, Spremulli LL, Agrawal RK. Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proceedings of the National Academy of Sciences of the United States of America. 111: 7284-9. PMID 24799711 DOI: 10.1073/Pnas.1401657111 |
0.457 |
|
| 2014 |
Hayes RL, Noel JK, Whitford PC, Mohanty U, Sanbonmatsu KY, Onuchic JN. Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. Biophysical Journal. 106: 1508-19. PMID 24703312 DOI: 10.1016/J.Bpj.2014.01.042 |
0.76 |
|
| 2014 |
Kirmizialtin S, Sanbonmatsu KY. Molecular Dynamics Simulations of Ribosomes: Integrating Theory and Experiment Biophysical Journal. 106: 39a. DOI: 10.1016/J.Bpj.2013.11.288 |
0.746 |
|
| 2013 |
Novikova IV, Hennelly SP, Sanbonmatsu KY. Tackling structures of long noncoding RNAs. International Journal of Molecular Sciences. 14: 23672-84. PMID 24304541 DOI: 10.3390/Ijms141223672 |
0.826 |
|
| 2013 |
Whitford PC, Sanbonmatsu KY. Simulating movement of tRNA through the ribosome during hybrid-state formation. The Journal of Chemical Physics. 139: 121919. PMID 24089731 DOI: 10.1063/1.4817212 |
0.738 |
|
| 2013 |
Novikova IV, Dharap A, Hennelly SP, Sanbonmatsu KY. 3S: shotgun secondary structure determination of long non-coding RNAs. Methods (San Diego, Calif.). 63: 170-7. PMID 23927838 DOI: 10.1016/J.Ymeth.2013.07.030 |
0.811 |
|
| 2013 |
Whitford PC, Blanchard SC, Cate JH, Sanbonmatsu KY. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. Plos Computational Biology. 9: e1003003. PMID 23555233 DOI: 10.1371/Journal.Pcbi.1003003 |
0.664 |
|
| 2013 |
Novikova IV, Hennelly SP, Tung CS, Sanbonmatsu KY. Rise of the RNA machines: exploring the structure of long non-coding RNAs. Journal of Molecular Biology. 425: 3731-46. PMID 23467124 DOI: 10.1016/J.Jmb.2013.02.030 |
0.818 |
|
| 2013 |
Hennelly SP, Novikova IV, Sanbonmatsu KY. The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch. Nucleic Acids Research. 41: 1922-35. PMID 23258703 DOI: 10.1093/Nar/Gks978 |
0.793 |
|
| 2013 |
Noel JK, Sanbonmatsu KY, Whitford PC. 35 The energy landscapes of ribosome function Journal of Biomolecular Structure and Dynamics. 31: 21-22. DOI: 10.1080/07391102.2013.786468 |
0.694 |
|
| 2012 |
Novikova IV, Hennelly SP, Sanbonmatsu KY. Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? Bioarchitecture. 2: 189-99. PMID 23267412 DOI: 10.4161/bioa.22592 |
0.819 |
|
| 2012 |
Whitford PC, Sanbonmatsu KY, Onuchic JN. Biomolecular dynamics: order-disorder transitions and energy landscapes. Reports On Progress in Physics. Physical Society (Great Britain). 75: 076601. PMID 22790780 DOI: 10.1088/0034-4885/75/7/076601 |
0.711 |
|
| 2012 |
Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. Journal of the American Chemical Society. 134: 12043-53. PMID 22612276 DOI: 10.1021/Ja301454U |
0.814 |
|
| 2012 |
Shi X, Khade PK, Sanbonmatsu KY, Joseph S. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. Journal of Molecular Biology. 419: 125-38. PMID 22459262 DOI: 10.1016/J.Jmb.2012.03.016 |
0.456 |
|
| 2012 |
Novikova IV, Hennelly SP, Sanbonmatsu KY. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Research. 40: 5034-51. PMID 22362738 DOI: 10.1093/Nar/Gks071 |
0.823 |
|
| 2012 |
Sanbonmatsu KY. Computational studies of molecular machines: the ribosome. Current Opinion in Structural Biology. 22: 168-74. PMID 22336622 DOI: 10.1016/J.Sbi.2012.01.008 |
0.481 |
|
| 2012 |
Ahmed A, Whitford PC, Sanbonmatsu KY, Tama F. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. Journal of Structural Biology. 177: 561-70. PMID 22019767 DOI: 10.1016/J.Jsb.2011.10.002 |
0.662 |
|
| 2012 |
Hayes RL, Onuchic J, Noel J, Sanbonmatsu K, Mohanty U. Glass-Like Behavior of Magnesium Ions Inside RNA APTamers Biophysical Journal. 102: 646a. DOI: 10.1016/J.Bpj.2011.11.3519 |
0.651 |
|
| 2012 |
Novikova IV, Hennelly SP, Sanbonmatsu KY. Biochemical Studies of a Long Noncoding RNA Involved in Breast Cancer Biology Biophysical Journal. 102: 639a. DOI: 10.1016/J.Bpj.2011.11.3479 |
0.504 |
|
| 2012 |
Whitford PC, Sanbonmatsu K. Probing the Energy Landscape of Ribosome Function Through Simulation Biophysical Journal. 102: 39a. DOI: 10.1016/J.Bpj.2011.11.242 |
0.733 |
|
| 2012 |
Sanbonmatsu KY, Blanchard SC, Whitford PC. Dynamics of very large systems: The ribosome Comprehensive Biophysics. 9: 76-85. DOI: 10.1016/B978-0-12-374920-8.00907-3 |
0.597 |
|
| 2011 |
Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Excited states of ribosome translocation revealed through integrative molecular modeling. Proceedings of the National Academy of Sciences of the United States of America. 108: 18943-8. PMID 22080606 DOI: 10.1073/Pnas.1108363108 |
0.81 |
|
| 2011 |
Zhang Z, Sanbonmatsu KY, Voth GA. Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. Journal of the American Chemical Society. 133: 16828-38. PMID 21910449 DOI: 10.1021/Ja2028487 |
0.545 |
|
| 2011 |
Hennelly SP, Sanbonmatsu KY. Tertiary contacts control switching of the SAM-I riboswitch. Nucleic Acids Research. 39: 2416-31. PMID 21097777 DOI: 10.1093/Nar/Gkq1096 |
0.773 |
|
| 2011 |
Ham M, Brumby S, Ji Z, Sanbonmatsu K, Kenyon G, George J, Bettencourt L. Task-specific saliency from sparse, hierarchical models of visual cortex compared to eye-tracking data for object detection in natural video sequences Journal of Vision. 11: 1281-1281. DOI: 10.1167/11.11.1281 |
0.329 |
|
| 2011 |
Whitford PC, Spahn CM, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Revealing the Energy Landscapes of Ribosome Function Biophysical Journal. 100: 238a. DOI: 10.1016/J.Bpj.2010.12.1517 |
0.769 |
|
| 2010 |
Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature. 468: 713-6. PMID 21124459 DOI: 10.1038/Nature09547 |
0.731 |
|
| 2010 |
Whitford PC, Onuchic JN, Sanbonmatsu KY. Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. Journal of the American Chemical Society. 132: 13170-1. PMID 20806913 DOI: 10.1021/Ja1061399 |
0.707 |
|
| 2010 |
Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT. Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure (London, England : 1993). 18: 787-97. PMID 20637415 DOI: 10.1016/J.Str.2010.04.006 |
0.77 |
|
| 2010 |
Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN. SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Research. 38: W657-61. PMID 20525782 DOI: 10.1093/Nar/Gkq498 |
0.764 |
|
| 2010 |
Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. Rna (New York, N.Y.). 16: 1196-204. PMID 20427512 DOI: 10.1261/Rna.2035410 |
0.772 |
|
| 2010 |
Munro JB, Altman RB, Tung CS, Sanbonmatsu KY, Blanchard SC. A fast dynamic mode of the EF-G-bound ribosome. The Embo Journal. 29: 770-81. PMID 20033061 DOI: 10.1038/Emboj.2009.384 |
0.345 |
|
| 2010 |
Munro JB, Altman RB, Tung CS, Cate JH, Sanbonmatsu KY, Blanchard SC. Spontaneous formation of the unlocked state of the ribosome is a multistep process. Proceedings of the National Academy of Sciences of the United States of America. 107: 709-14. PMID 20018653 DOI: 10.1073/Pnas.0908597107 |
0.374 |
|
| 2010 |
Sanbonmatsu K, Bennett R, Barr S, Renaudo C, Ham M, Gintautas V, Brumby S, George J, Kenyon G, Bettencourt L. Comparing Speed-of-Sight studies using rendered vs. natural images Journal of Vision. 10: 986-986. DOI: 10.1167/10.7.986 |
0.195 |
|
| 2010 |
Vaiana AC, Grubmueller H, Sanbonmatsu KY. Simulations of the Bacterial Ribosomal Decoding Switch Biophysical Journal. 98: 260a. DOI: 10.1016/J.BPJ.2009.12.1415 |
0.305 |
|
| 2009 |
Munro JB, Sanbonmatsu KY, Spahn CM, Blanchard SC. Navigating the ribosome's metastable energy landscape. Trends in Biochemical Sciences. 34: 390-400. PMID 19647434 DOI: 10.1016/J.Tibs.2009.04.004 |
0.412 |
|
| 2009 |
Whitford PC, Schug A, Saunders J, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophysical Journal. 96: L7-9. PMID 19167285 DOI: 10.1016/J.Bpj.2008.10.033 |
0.8 |
|
| 2009 |
Vaiana AC, Sanbonmatsu KY. Stochastic gating and drug-ribosome interactions. Journal of Molecular Biology. 386: 648-61. PMID 19146858 DOI: 10.1016/j.jmb.2008.12.035 |
0.797 |
|
| 2009 |
Whitford PC, Noel JK, Gosavi S, Schug A, Sanbonmatsu KY, Onuchic JN. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins. 75: 430-41. PMID 18837035 DOI: 10.1002/Prot.22253 |
0.714 |
|
| 2009 |
Whitford PC, Schug A, Noel JK, Gosavi S, Hennelly SP, Sanbonmatsu KY, Onuchic JN. All-atom Models For RNA And Proteins: Simulating Folding And Function Biophysical Journal. 96: 555a. DOI: 10.1016/J.Bpj.2008.12.3648 |
0.763 |
|
| 2009 |
Munro JB, Altman RB, Tung C, Cate JH, Sanbonmatsu KY, Blanchard SC. Dynamic Mode Switching and Loosely Coupled Conformational Events Observed in Single Ribosomes Biophysical Journal. 96: 580a. DOI: 10.1016/J.Bpj.2008.12.3034 |
0.416 |
|
| 2008 |
Munro JB, Vaiana A, Sanbonmatsu KY, Blanchard SC. A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. Biopolymers. 89: 565-77. PMID 18286627 DOI: 10.1002/Bip.20961 |
0.791 |
|
| 2007 |
Sanbonmatsu KY, Tung CS. High performance computing in biology: multimillion atom simulations of nanoscale systems. Journal of Structural Biology. 157: 470-80. PMID 17187988 DOI: 10.1016/J.Jsb.2006.10.023 |
0.452 |
|
| 2006 |
Sanbonmatsu KY. Energy landscape of the ribosomal decoding center. Biochimie. 88: 1053-9. PMID 16905237 DOI: 10.1016/j.biochi.2006.06.012 |
0.412 |
|
| 2006 |
Sanbonmatsu KY. Alignment/misalignment hypothesis for tRNA selection by the ribosome. Biochimie. 88: 1075-89. PMID 16890341 DOI: 10.1016/j.biochi.2006.07.002 |
0.408 |
|
| 2006 |
Sanbonmatsu KY, Tung CS. Large-scale simulations of the ribosome: A new landmark in computational biology Journal of Physics: Conference Series. 46: 334-342. DOI: 10.1088/1742-6596/46/1/047 |
0.394 |
|
| 2005 |
Sanbonmatsu KY, Joseph S, Tung CS. Simulating movement of tRNA into the ribosome during decoding. Proceedings of the National Academy of Sciences of the United States of America. 102: 15854-9. PMID 16249344 DOI: 10.1073/Pnas.0503456102 |
0.474 |
|
| 2004 |
Tung CS, Sanbonmatsu KY. Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophysical Journal. 87: 2714-22. PMID 15454463 DOI: 10.1529/biophysj.104.040162 |
0.42 |
|
| 2003 |
Gnanakaran S, Nymeyer H, Portman J, Sanbonmatsu KY, GarcÃa AE. Peptide folding simulations. Current Opinion in Structural Biology. 13: 168-74. PMID 12727509 DOI: 10.1016/S0959-440X(03)00040-X |
0.317 |
|
| 2003 |
Sanbonmatsu KY, Joseph S. Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. Journal of Molecular Biology. 328: 33-47. PMID 12683995 DOI: 10.1016/S0022-2836(03)00236-5 |
0.337 |
|
| 2002 |
Tung CS, Joseph S, Sanbonmatsu KY. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nature Structural Biology. 9: 750-5. PMID 12244297 DOI: 10.1038/Nsb841 |
0.406 |
|
| 2002 |
GarcÃa AE, Sanbonmatsu KY. Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds. Proceedings of the National Academy of Sciences of the United States of America. 99: 2782-7. PMID 11867710 DOI: 10.1073/Pnas.042496899 |
0.259 |
|
| 2002 |
Sanbonmatsu KY, GarcÃa AE. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins. 46: 225-34. PMID 11807951 DOI: 10.1002/Prot.1167 |
0.469 |
|
| 2001 |
Sanbonmatsu KY, Murillo MS. Shear viscosity of strongly coupled Yukawa systems on finite length scales. Physical Review Letters. 86: 1215-8. PMID 11178047 DOI: 10.1103/Physrevlett.86.1215 |
0.375 |
|
| 2001 |
GarcÃa AE, Sanbonmatsu KY. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins. 42: 345-54. PMID 11151006 DOI: 10.1002/1097-0134(20010215)42:3<345::Aid-Prot50>3.0.Co;2-H |
0.225 |
|
| 2001 |
Sanbonmatsu KY, Newman DL, Goldman MV. Quasi-linear Zakharov simulations of Langmuir turbulence at rocket altitudes in the auroral ionosphere Journal of Geophysical Research: Space Physics. 106: 10519-10535. DOI: 10.1029/2000Ja000270 |
0.66 |
|
| 2000 |
Sanbonmatsu KY, Vu HX, DuBois DF, Bezzerides B. Quantitative comparison of reduced-description particle-in-cell and quasilinear-Zakharov models for parametrically excited Langmuir turbulence Physics of Plasmas. 7: 2824-2841. DOI: 10.1063/1.874132 |
0.678 |
|
| 2000 |
Sanbonmatsu KY, Vu HX, Bezzerides B, DuBois DF. The effect of kinetic processes on Langmuir turbulence Physics of Plasmas. 7: 1723-1731. DOI: 10.1063/1.873991 |
0.676 |
|
| 2000 |
Sanbonmatsu KY, Thode LE, Vu HX, Murillo MS. Comparison of molecular dynamics and particle-in-cell
simulations for strongly coupled plasmas Le Journal De Physique Iv. 10: Pr5-259-Pr5-262. DOI: 10.1051/Jp4:2000546 |
0.276 |
|
| 2000 |
Vu H, Sanbonmatsu K, Bezzerides B, DuBois D. Laying a foundation for laser-plasma modeling for the national ignition facility Computer Physics Communications. 127: 71-90. DOI: 10.1016/S0010-4655(00)00117-X |
0.668 |
|
| 1999 |
Sanbonmatsu K, Vu H, DuBois D, Bezzerides B. New Paradigm for the Self-Consistent Modeling of Wave-Particle and Wave-Wave Interactions in the Saturation of Electromagnetically Driven Parametric Instabilities Physical Review Letters. 82: 932-935. DOI: 10.1103/PHYSREVLETT.82.932 |
0.672 |
|
| 1997 |
Sanbonmatsu KY, Doxas I, Goldman MV, Newman DL. Non-Markovian electron diffusion in the auroral ionosphere at high Langmuir-wave intensities Geophysical Research Letters. 24: 807-810. DOI: 10.1029/97Gl00669 |
0.661 |
|
| 1995 |
Sanbonmatsu KY, Goldman MV, Newman DL. Nonlinear coupling of lower hybrid waves to the kinetic low-frequency plasma response in the auroral ionosphere Geophysical Research Letters. 22: 2397-2400. DOI: 10.1029/95Gl02227 |
0.643 |
|
| 1992 |
Sanbonmatsu KY, Helfand DJ. A distance determination for the supernova remnant G27.4+0.0 and its central X-ray source The Astronomical Journal. 104: 2189. DOI: 10.1086/116393 |
0.206 |
|
| Show low-probability matches. |