Hawkes, E.J, Hennelly, S.P, Novikova, I.V, Irwin, J.A, Dean, C, and Sanbonmatsu, K.Y. (2016) COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. Cell Reports, published September 20, 2016. doi:10.1016/j.celrep.2016.08.045. View PDF »
Xue, Z, Hennelly, S.P, Doyle, B, Gulati, A.A, Novikova, I.V, Sanbonmatsu, K.Y, and Boyer, L.A. (2016) A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Molecular Cell, published September 8, 2016. doi:10.1016/j.molcel.2016.08.010. View article »
Bascom, G.D, Sanbonmatsu, K.Y, and Schlick, T. (2016) Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. The Journal of Physical Chemistry B 120 (33), 8642-8653, published May 24, 2016. doi:10.1021/acs.jpcb.6b03197. View article »
Sanbonmatsu, K.Y. (2016) Towards Structural Classification of Long Non-Coding RNAs. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (1), 41-45, published January 1, 2016. doi:10.1016/j.bbagrm.2015.09.011. View article »
Kirmizialtin, S, Loerke, J, Behrmann, E, Spahn, C.M.T, and Sanbonmatsu, K.Y. (2015) Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods in Enzymology 558, 497-514, published May 9, 2015. doi:10.1016/bs.mie.2015.02.011. View PDF »
Kirmizialtin, S, Hennelly, S.P, Schug, A, Onuchic, J.N, and Sanbonmatsu, K.Y. (2015) Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT. Methods in Enzymology 553, 215-234, published February 7, 2015. doi:10.1016/bs.mie.2014.10.061. View PDF »
Krishnamurthy. M, Hennelly, S.P, Dale, T, Starkenburg, S.R, Martí-Arbona, R, Fox, D.T, Twary, S.N, Sanbonmatsu, K.Y, and Unkefer, C.J. (2015) Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression. American Chemical Society Synthetic Biology 4 (12), 1326-1334, published July 27, 2015. doi:10.1021/acssynbio.5b00041. View PDF »
Hayes, R.L, Noel, J.K, Mandic, A, Whitford, P.C, Sanbonmatsu, K.Y, Mohanty, U, and Onuchic, J.N. (2015) Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Physical Review Letters 114 (25), 258105, published June 26, 2015. doi:10.1016/j.molcel.2014.12.016. View PDF »
Muhs, M, Hilal, T, Mielke, T, Skabkin, M.A, Sanbonmatsu, K.Y, Pestova, T.V, and Spahn, C.M.T. (2015) Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES. Molecular Cell 57 (3), 422-432, published February 5, 2015. doi:10.1016/j.molcel.2014.12.016. View PDF »
Budkevich, T.V, Giesebrecht, J, Behrmann, E, Loerke, J, Ramrath, D.J.F, Mielke, T, Ismer, J, Hildebrand, P.W, Tung, C-S, Nierhaus, K.H, Sanbonmatsu, K.Y, and Spahn, C.M.T. (2014) Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement. Cell 158 (1), 121-131, published July 3, 2014. doi:10.1016/j.cell.2014.04.044. View PDF »
Sanbonmatsu, K.Y. (2014) 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 (19), 3197-3200, published September 2014. doi:10.1016/j.jmb.2014.07.005. View PDF »
Sanbonmatsu, K.Y. (2014) Dynamics of Riboswitches: Molecular Simulations. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1839 (10), 1046-1050. published October 2014. doi:10.1016/j.bbagrm.2014.06.010. View PDF »
Kaushal, P.S, Sharma, M.R, Booth, T.M, Haque, E.M, Tung, C-S, Sanbonmatsu, K.Y, Spremulli, L.L, and Agrawal, R.K. (2014) Cryo-EM Structure of the Small Subunit of the Mammalian Mitochondrial Ribosome. Proceedings of the National Academy of Sciences 111 (20), 7284-7289, published May 20, 2014. doi:10.1073/pnas.1401657111. View PDF »
Hayes, R.L, Noel, J.K, Whitford, P.C, Mohanty, U, Sanbonmatsu, K.Y, and Onuchic, J.N. (2014) Reduced Model Captures Mg(2+)-RNA Interaction Free Energy of Riboswitches. Biophysical journal 106 (7), 1508-1519, published April 1, 2014. doi:10.1016/j.bpj.2014.01.042.View PDF »
Novikova, I.V, Hennelly, S.P, Tung, C-S, and Sanbonmatsu, K.Y. (2013) Rise of the RNA Machines: Structural Probing of Long Non-Coding RNAs. Journal of Molecular Biology, 425(19)3731-3746, published October 9, 2013. doi:10.1016/j.jmb.2013.02.030. View PDF »
Novikova, I.V, Dharap, A, Hennelly, S.P, and Sanbonmatsu, K.Y. (2013) Shotgun Secondary Structure Determination for Long Non-Coding RNAs. Methods, 63 (2), 170-177, published August 6, 2013. doi:10.1016/j.ymeth.2013.07.030. View PDF »
Novikova, I.V, Hennelly, S.P, and Sanbonmatsu, K.Y. (2014) Tackling Structures of Long Non-Coding RNAs. International Journal of Molecular Science 14 (12), 23672-23684, published December 4, 2014. doi:10.3390/ijms141223672. View PDF »
Whitford, P.C. and Sanbonmatsu, K.Y. (2013) Simulating Movement of tRNA Through the Ribosome During Hybrid-State Formation. Journal of chemical physics 139, 121919, published September 28, 2013. doi:10.1063/1.4817212. View PDF »
Whitford, P.C, Blanchard, S.C, Cate, J.H.D, and Sanbonmatsu, K.Y. (2013) Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome. PLoS computational biology 9 (3), e1003003, published March 21, 2013. doi:10.1371/journal.pcbi.1003003. View PDF »
Hennelly, S.P, Novikova, I.V, and Sanbonmatsu, K.Y. (2012) The Expression Platform and the Aptamer: Cooperativity Between Mg2+ and Ligand in the SAM-I Riboswitch. Nucleic acids research 41 (3), 1922-1935, published December 20, 2012. doi:10.1093/nar/gks978. View PDF »
Sanbonmatsu, K.Y, Blanchard, S.C, and Whitford, P.C. (2012) Molecular Dynamics Simulations of the Ribosome. Biophysical Approaches to Translational Control of Gene Expression, 51-68, published August 24, 2012. doi:10.1007/978-1-4614-3991-2_3. View PDF »
Novikova, I.V, Hennelly, S.P, and Sanbonmatsu, K.Y. (2012) Sizing Up Long Non-Coding RNAs: Do LncRNAs Have Secondary and Tertiary Structure? Bio Architecture 2 (6), 189-199, published November 1, 2012. doi:10.4161/bioa.22592. View PDF »
Hayes, R.L, Noel, J.K, Mohanty, U, Whitford, P.C, Hennelly, S.P, Onuchic, J.N, and Sanbonmatsu, K.Y. (2012) Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch. Journal of the American Chemical Society 134 (29), 12043-12053, published July 16, 2012. doi:10.1021/ja301454u. View PDF »
Whitford, P.C, Sanbonmatsu, K.Y, and Onuchic, J.N. (2012) Biomolecular Dynamics: Order–Disorder Transitions and Energy Landscapes. Reports on Progress in Physics 75 (7), 076601, published June 28, 2012. doi:10.1088/0034-4885/75/7/076601. View PDF »
Novikova, I.V, Hennelly, S.P, and Sanbonmatsu, K.Y. (2012) Structural Architecture of the Human Long Non-Coding RNA, Steroid Receptor RNA Activator. Nucleic Acids Research 40 (11), 5034-5051, published February 22, 2012. doi:10.1093/nar/gks071. View PDF »
Sanbonmatsu, K.Y. (2012) Computational Studies of Molecular Machines: The Ribosome. Current Opinion in Structural Biology 22 (2), 168-174, published February 13, 2012. doi:10.4161/bioa.22592. View PDF »
Whitford, P.C, Ahmed, A, Yu, Y, Hennelly, S.P, Tama, F, Spahn, C.M.T, Onuchic, J.N, and Sanbonmatsu, K.Y. (2011) Excited States of Ribosome Translocation Revealed through Integrative Molecular Modeling. Proceedings of the National Academy of Sciences 108 (47), 18943-18948, published November 11, 2011. doi:10.1073/pnas.1108363108. View PDF »
Ahmed, A, Whitford, P.C, Sanbonmatsu, K.Y, and Tama, F. (2011) Consensus Among Flexible Fitting Approaches Improves the Interpretation of Cryo-EM Data. Journal of Structural Biology 177 (2), 561-570, published October 13, 2011. doi:10.1016/j.jsb.2011.10.002. View PDF »
Zhang, Z, Sanbonmatsu, K.Y, and Voth, G.A. (2011) Key Inter-Molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis. Journal of the American Chemical Society 133 (42), 16828-16838, published October 3, 2011. doi:10.1021/ja2028487. View PDF »
Sanbonmatsu, K.Y, Blanchard, S.C, and Whitford, P.C. (2011) Information Processing by Nanomachines. Molecular Machines 67, published 2011. View PDF »
Hennelly, S.P, and Sanbonmatsu, K.Y. (2010) Tertiary Contacts Control Switching of the SAM-I Riboswitch. Nucleic Acids Research 39 (6), 2416-2431, published November 19, 2010. doi:10.1093/nar/gkq1096. View PDF »
Whitford, P.C, Altman, R.B, Geggier, P, Terry, D.S, Munro, J.B, Onuchic, J.N, Spahn, C.M.T, Sanbonmatsu, K.Y, and Blanchard, S.C. (2011) Dynamic Views of Ribosome Function: Energy Landscapes and Ensembles. Ribosomes, 303-319, published 2010. doi:10.1007/978-3-7091-0215-2_24. View PDF »
Ratje, A.H, Loerke, J, Mikolajka, A, Brünner, M, Hildebrand, P.W, Starosta, A.L, Dönhöfer, A, Connell, S.R, Fucini, P, Mielke, T, Whitford, P.C, Onuchic, J.N, Yu, Y, Sanbonmatsu, K.Y, Hartmann, R.K, Penczek, P.A, Wilson, D.N, and Spahn, C.M.T. (2010) Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites. Nature 468 (7324), 713-716, published December 2, 2010. doi:10.1038/nature09547. View PDF »
Whitford, P.C, Onuchic, J.N, and Sanbonmatsu, K.Y. (2010) Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome. Journal of the American Chemical Society 132 (38), 13170-13171, published September 29, 2010. doi:10.1021/ja1061399. View PDF »
Stoddard, C.D, Montange, R.K, Hennelly, S.P, Rambo, R.P, Sanbonmatsu, K.Y, and Batey, R.T. (2010) Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain. Structure 18 (7), 787-797, published July 14, 2010. doi:10.1016/j.str.2010.04.006. View PDF »
Noel, J.K, Whitford, P.C, Sanbonmatsu, K.Y, and Onuchic, J.N. (2010) SMOG@ctbp: Simplified Deployment of structure-Based Models in GROMACS. Nucleic acids research 38 (suppl 2), W657-W661, published June 4, 2010. doi:10.1093/nar/gkq498. View PDF »
Whitford, P.C, Geggier, P, Altman, R.B, Blanchard, S.C, Onuchic, J.N, and Sanbonmatsu, K.Y. (2010) Accommodation of Aminoacyl-tRNA Into the Ribosome Involves Reversible Excursions Along Multiple Pathways. RNA 16 (6), 1196-1204, published June 2010. doi:10.1261/rna.2035410. View PDF »
Munro, J.B, Altman, R.B, Tung, C-S, Cate, J.H.D, Sanbonmatsu, K.Y, and Blanchard, S.C. (2009) Spontaneous Formation of the Unlocked State of the Ribosome is a Multistep Process. Proceedings of the National Academy of Sciences 107 (2), 709-714, published December 17, 2009. doi:10.1073/pnas.0908597107. View PDF »
Munro, J.B, Altman, R.B, Tung, C-S, Sanbonmatsu, K.Y, and Blanchard, S.C. (2009) A Fast Dynamic Mode of the EF-G-Bound Ribosome. The EMBO journal 29 (4), 770-781, published December 24, 2009. doi:10.1038/emboj.2009.384. View PDF »
Munro, J.B, Altman, R.B, Tung, C-S, Sanbonmatsu, K.Y, and Blanchard, S.C. (2009) Navigating the Ribosome's Metastable Energy Landscape. The EMBO journal 29 (4), 770-781, published December 24, 2009. doi:10.1038/emboj.2009.384. View PDF »
Vaiana, A.C. and Sanbonmatsu, K.Y. (2009) Stochastic Gating and Drug–Ribosome Interactions. Journal of Molecular Biology 386 (3), 648-661, published February 27, 2009. doi:10.1016/j.jmb.2008.12.035. View PDF »
Whitford, P.C, Schug, A, Saunders, J, Hennelly, S.P, Onuchic, J.N, and Sanbonmatsu, K.Y. (2009) Nonlocal Helix Formation is Key to Understanding S-Adenosylmethionine-1 Riboswitch Function. Biophysical journal 96 (2), L7-L9, published January 21, 2009. doi:10.1016/j.bpj.2008.10.033. View PDF »
Whitford, P.C, Noel, J.K, Gosavi, S, Schug, A, Sanbonmatsu, K.Y, and Onuchic, J.N. (2008) All-atom Models For RNA And Proteins: Simulating Folding And Function. Proteins: Structure, Function, and Bioinformatics 75 (2), 430-441, published September 2, 2008. doi:10.1002/prot.22253. View PDF »
Munro, J.B, Vaiana, A, Sanbonmatsu, K.Y, and Blanchard, S.C. (2008) A New View of Protein Synthesis: Mapping the Free Energy Landscape of the Ribosome Using Single-Molecule FRET. Biopolymers 89 (7), 565-577, published July 2008. doi:10.1002/bip.20961. View PDF »
Ming, D, Wall, M.E, and Sanbonmatsu, K.Y. (2007) Domain Motions of Argonaute, the Catalytic Engine of RNA Interference. BMC bioinformatics 8 (1), 470, published November 30, 2007. doi:10.1186/1471-2105-8-470. View PDF »
Sanbonmatsu, K.Y. and Tung, C-S. (2007) High Performance Computing in Biology: Multimillion Atom Simulations of Nanoscale Systems. Journal of structural biology 157 (3), 470-480, published March 2007. doi:10.1016/j.jsb.2006.10.023. View PDF »
Sanbonmatsu, K.Y. and Tung, C-S. (2006) Large-Scale Simulations of the Ribosome: A New Landmark in Computational Biology. Journal of Physics: Conference Series 46 (1), 334-342, published 2006. View PDF »
Sanbonmatsu, K.Y. (2006) Alignment/Misalignment Hypothesis for tRNA Selection by the Ribosome. Biochimie 88 (8), 1075-1089, published August 2006. doi:10.1016/j.biochi.2006.07.002. View PDF »
Sanbonmatsu, K.Y. (2006) Energy Landscape of the Ribosomal Decoding Center. Biochimie 88 (8), 1053-1059, published August 2006. doi:10.1016/j.biochi.2006.07.002. View PDF »
Sanbonmatsu, K.Y. (2006) Using Computer Simulations to Study Decoding by the Ribosome. Computational Studies of RNA and DNA, 327-342, published 2006. doi:10.1007/978-1-4020-4851-3_13. View article »
Sanbonmatsu, K.Y, Joseph, S, and Tung, C-S. (2005) Simulating Movement of tRNA Into the Ribosome During Decoding. Proceedings of the National Academy of Sciences 102 (44), 15854-15859, published October 25, 2005. doi:10.1073/pnas.0503456102. View PDF »
Tung, C-S. and Sanbonmatsu, K.Y. (2004) Atomic Model of the Thermus thermophilus 70S Ribosome Developed in Silico. Biophysical journal 87 (4), 2714-2722, published October 2004. doi:10.1529/biophysj.104.040162. View PDF »
Gnanakaran, S, Nymeyer, H, Portman, J, Sanbonmatsu, K.Y, and Garcıa, A.E. (2003) Peptide Folding Simulations. Current Opinion in Structural Biology 13 (2), 168-174, published April 2003. doi:10.1016/S0959-440X(03)00040-X. View PDF »
Sanbonmatsu, K.Y. and Joseph, S. (2003) Understanding Discrimination by the Ribosome: Stability Testing and Groove Measurement of Codon–Anticodon Pairs. Journal of Molecular Biology 328 (1), 33-47, published April 18, 2003. doi:10.1016/S0022-2836(03)00236-5. View PDF »
Tung, C-S, Joseph, S, and Sanbonmatsu, K.Y. (2002) All-Atom Homology Model of the Escherichia coli 30S Ribosomal Subunit. Nature Structural & Molecular Biology 9 (10), 750-755, published September 16, 2002. doi:10.1038/nsb841. View PDF »
García, A.E. and Sanbonmatsu, K.Y. (2002) Alpha-Helical Stabilization by Side Chain Shielding of Backbone Hydrogen Bonds. Proceedings of the National Academy of Sciences 99 (5), 2782-2787, published February 26, 2002. doi:10.1073/pnas.042496899. View PDF »
Sanbonmatsu, K.Y. and García, A.E. (2001) Structure of Met-Enkephalin in Explicit Aqueous Solution Using Replica Exchange Molecular Dynamics. Proteins: Structure, Function, and Bioinformatics 46 (2), 225-234, published December 7, 2001. doi:10.1002/prot.1167. View PDF »
Sanbonmatsu, K.Y, Newman, D.L, and Goldman, M.V. (2001) Quasi-Linear Zakharov Simulations of Langmuir Turbulence at Rocket Altitudes in the Auroral Ionosphere. Journal of geophysical research 106 (A6), 10519-10535, published June 1, 2001. doi:10.1029/2000JA000270. View PDF »
Sanbonmatsu, K.Y. and Murillo, M.S. (2001) Shear Viscosity of Strongly Coupled Yukawa Systems on Finite Length Scales. Physical Review Letters 86 (7), 1215-1218, published February 12, 2001. doi:10.1103/PhysRevLett.86.1215. View PDF »
García, A.E. and Sanbonmatsu, K.Y. (2001) Exploring the Energy Landscape of a Beta Hairpin in Explicit Solvent. Proteins: Structure, Function, and Bioinformatics 42 (3), 345-354, published February 15, 2001. doi:10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H. View article »
Vu, H.X, Sanbonmatsu, K.Y, Bezzerides, B, and DuBois, D.F. (2000) Laying a Foundation for Laser-Plasma Modeling for the National Ignition Facility. Computer Physics Communications 127, 71-90, published 2000. doi:10.1016/S0010-4655(00)00117-X. View article »
Sanbonmatsu, K.Y, Thode, L.E, Vu, H.X, and Murillo, M.S. (2000) Comparison of Molecular Dynamics and Particle-in-Cell Simulations for Strongly Coupled Plasmas. Journal de Physique IV 10 (PR5), 259-262, published March 2000. doi:10.1051/jp4:2000546. View article »
Sanbonmatsu, K.Y, Vu, H.X, DuBois, D.F, and Bezzerides, B. (2000) Quantitative Comparison of Reduced-Description Particle-in-Cell and Quasilinear-Zakharov Models for Parametrically Excited Langmuir Turbulence. Physics of Plasmas 7, 2824, published March 23, 2000. doi:10.1063/1.874132. View article »
Sanbonmatsu, K.Y, Vu, H.X, Bezzerides, B, and DuBois, D.F. (2000) The Effect of Kinetic Processes on Langmuir Turbulence. Physics of Plasmas 7, 1723, published January 27, 2000. doi:10.1063/1.873991. View article »
Sanbonmatsu, K.Y, Vu, H.X, DuBois, D.F, and Bezzerides, B. (1999) New Paradigm for the Self-Consistent Modeling of Wave-Particle and Wave-Wave Interactions in the Saturation of Electromagnetically Driven Parametric Instabilities. Physicsal Review Letters 82 (5), 932-935, published February 1, 1999. doi:10.1103/PhysRevLett.82.932. View article »
Sanbonmatsu, K.Y, Doxas, I, Goldman, M.V, and Newman, D.L. (1997) Non-Markovian Electron Diffusion in the Auroral Ionosphere at High Langmuir-Wave Intensities. Geophysicsal Research Letters 24 (7), 807-810, published April 1, 1997. doi:10.1029/97GL00669. View PDF »
Sanbonmatsu, K.Y, Goldman, M.V, and Newman, D.L. (1995) Nonlinear Coupling of Lower Hybrid Waves to the Kinetic Low-Frequency Plasma Response in the Auroral Ionosphere. Geophysicsal Research Letters 22 (17), 2397-2400, published September 1, 1995. doi:10.1029/95GL02227. View article »
Sanbonmatsu, K.Y. and Helfand, D.J. (1992) A Distance Determination for the Supernova Remnant G27.4+0.0 and its Central X-ray Source. Astronomical Journal 104 (6), 2189-2192, published December 1992. ads:1992AJ....104.2189S. View article »