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List of works by Karissa Sanbonmatsu

3S: shotgun secondary structure determination of long non-coding RNAs.

scientific article published on 6 August 2013

9.5 Dynamics of Very Large Systems: The Ribosome

article

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.

scientific article published on 31 August 2016

A distance detemination for the supernova remnant G27.4+0.0 and its central X-ray source

scientific article published in January 1992

A fast dynamic mode of the EF-G-bound ribosome.

scientific article

A magnesium-induced triplex pre-organizes the SAM-II riboswitch.

scientific article

A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.

scientific article

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

scientific article

Alignment/misalignment hypothesis for tRNA selection by the ribosome

scientific article published on 26 July 2006

All-atom homology model of the Escherichia coli 30S ribosomal subunit.

scientific article

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

scientific article

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

scientific article

Atomic model of the Thermus thermophilus 70S ribosome developed in silico

scientific article

Biomolecular dynamics: order–disorder transitions and energy landscapes ⬇️

scientific article published on June 28, 2012

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.

scientific article published in September 2016

Computational studies of molecular machines: the ribosome ⬇️

scientific article published on February 13, 2012

Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome

scientific article

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome

scientific article

Consensus among flexible fitting approaches improves the interpretation of cryo-EM data

scientific article

Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch

scientific article published in July 2017

Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES.

scientific article published on 15 January 2015

Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome

scientific article

Cryo_fit: Democratization of flexible fitting for cryo-EM

scientific article published on 03 July 2019

Domain motions of Argonaute, the catalytic engine of RNA interference

scientific article

Dynamics of riboswitches: Molecular simulations.

scientific article published on 19 June 2014

Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection

scientific article published on 13 February 2020

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

scientific article published on 05 February 2020

Energy landscape of the ribosomal decoding center

scientific article published on 26 July 2006

Excited states of ribosome translocation revealed through integrative molecular modeling ⬇️

scientific article published on November 11, 2011

Exploring the energy landscape of a beta hairpin in explicit solvent

scientific article published on 01 February 2001

Flipping through the genetic code: new developments in discrimination between cognate and near-cognate tRNAs and the effect of antibiotics

scientific article published on 11 July 2014

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

scientific article

Functional Role of the Sarcin–Ricin Loop of the 23S rRNA in the Elongation Cycle of Protein Synthesis ⬇️

scientific article published on March 26, 2012

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages

scientific article

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.

scientific article

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

scientific article

High performance computing in biology: multimillion atom simulations of nanoscale systems

scientific article published on 10 November 2006

Identification and Characterization of a Class of MALAT1-like Genomic Loci

scientific article

Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

scientific article published on 7 February 2015

Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis

scientific article published on 3 October 2011

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR

scientific article published on 01 April 2019

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch ⬇️

scientific article published on July 16, 2012

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements.

scientific article

Modeling the NP-vRNA-Polymerase Complex in Atomic Detail

scientific article

Navigating the ribosome's metastable energy landscape

scientific article

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function

scientific article published on January 2009

Peptide folding simulations ⬇️

scientific article published on April 1, 2003

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps

scientific article published on 18 May 2020

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

scientific article published on 05 November 2020

Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches

scientific article published on April 2014

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

scientific article

Rise of the RNA machines: exploring the structure of long non-coding RNAs

scientific article published on 04 March 2013

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

scientific article

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations

scientific article published on 17 April 2019

Shear viscosity of strongly coupled Yukawa systems on finite length scales

scientific article published in February 2001

Simulating movement of tRNA into the ribosome during decoding

scientific article

Simulating movement of tRNA through the ribosome during hybrid-state formation

scientific article published on September 2013

Sizing up long non-coding RNAs: Do lncRNAs have secondary and tertiary structure? ⬇️

scientific article published on November 1, 2012

Spontaneous formation of the unlocked state of the ribosome is a multistep process

scientific article

Stalking Structure in Plant Long Noncoding RNAs

scientific article published on 01 January 2019

Stochastic gating and drug-ribosome interactions

scientific article published on 24 December 2008

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position

scientific article published on 29 August 2017

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator ⬇️

scientific article published on February 22, 2012

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

scientific article published in February 2002

Tackling structures of long noncoding RNAs

scientific article

Tertiary contacts control switching of the SAM-I riboswitch ⬇️

scientific article published on November 19, 2010

The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch ⬇️

scientific article published on December 20, 2012

Tools for the Cryo-EM Gold Rush: Going from the cryo-EM map to the atomistic model

scientific article published on 29 September 2017

Towards structural classification of long non-coding RNAs.

scientific article published on 29 October 2015

Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

scientific article

Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression.

scientific article published on 27 July 2015

Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs

scientific article published on 01 April 2003

Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions

scientific article

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

scientific article published on 09 January 2020

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