Karissa Sanbonmatsu
#98,970
Most Influential Person Now
American structural biologist
Karissa Sanbonmatsu's AcademicInfluence.com Rankings
Karissa Sanbonmatsuphysics Degrees
Physics
#6188
World Rank
#8098
Historical Rank
#1717
USA Rank
Biophysics
#408
World Rank
#420
Historical Rank
#69
USA Rank
Karissa Sanbonmatsubiology Degrees
Biology
#8982
World Rank
#12131
Historical Rank
#2384
USA Rank
Molecular Biology
#2611
World Rank
#2652
Historical Rank
#290
USA Rank
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Physics Biology
Karissa Sanbonmatsu's Degrees
- PhD Biophysics University of California, Berkeley
- Bachelors Physics University of California, Berkeley
Why Is Karissa Sanbonmatsu Influential?
(Suggest an Edit or Addition)According to Wikipedia, Karissa Y. Sanbonmatsu is an American structural biologist at Los Alamos National Laboratory. She works on the mechanism of non-coding RNA complexes including the ribosome, riboswitches, long non-coding RNAs, as well as chromatin. She was the first to perform an atomistic simulation of the ribosome, determine the secondary structure of an intact lncRNA and to publish a one billion atom simulation of a biomolecular complex.
Karissa Sanbonmatsu's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- α-Helical stabilization by side chain shielding of backbone hydrogen bonds (2002) (381)
- An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields (2009) (315)
- SMOG@ctbp: simplified deployment of structure-based models in GROMACS (2010) (279)
- Simulating movement of tRNA into the ribosome during decoding. (2005) (278)
- Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics (2002) (241)
- Structural architecture of the human long non-coding RNA, steroid receptor RNA activator (2012) (236)
- Exploring the energy landscape of a β hairpin in explicit solvent (2001) (233)
- Peptide folding simulations. (2003) (192)
- Free state conformational sampling of the SAM-I riboswitch aptamer domain. (2010) (185)
- Head swivel on the ribosome facilitates translocation via intra-subunit tRNA hybrid sites (2010) (184)
- Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. (2010) (177)
- High performance computing in biology: multimillion atom simulations of nanoscale systems. (2007) (154)
- Biomolecular dynamics: order–disorder transitions and energy landscapes (2012) (128)
- Spontaneous formation of the unlocked state of the ribosome is a multistep process (2009) (126)
- A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. (2016) (126)
- Navigating the ribosome's metastable energy landscape. (2009) (122)
- Sizing up long non-coding RNAs (2012) (121)
- Rise of the RNA machines: exploring the structure of long non-coding RNAs. (2013) (121)
- Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement (2014) (117)
- COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. (2016) (99)
- Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. (2009) (98)
- Excited states of ribosome translocation revealed through integrative molecular modeling (2011) (94)
- Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES. (2015) (82)
- A fast dynamic mode of the EF‐G‐bound ribosome (2010) (81)
- Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. (2012) (78)
- Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. (2012) (77)
- Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome (2013) (76)
- Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome (2014) (72)
- Tackling Structures of Long Noncoding RNAs (2013) (68)
- Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. (2003) (65)
- Computational studies of molecular machines: the ribosome. (2012) (63)
- Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations (2019) (61)
- Stochastic gating and drug-ribosome interactions. (2009) (59)
- All-atom homology model of the Escherichia coli 30S ribosomal subunit (2002) (59)
- Exploring the energy landscape of a beta hairpin in explicit solvent. (2001) (57)
- 3S: shotgun secondary structure determination of long non-coding RNAs. (2013) (51)
- Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. (2010) (48)
- Energy landscape of the ribosomal decoding center. (2006) (48)
- Identification and Characterization of a Class of MALAT1-like Genomic Loci. (2017) (46)
- Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. (2015) (45)
- Shear viscosity of strongly coupled Yukawa systems on finite length scales. (2001) (45)
- A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. (2008) (44)
- The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch (2012) (44)
- Atomic model of the Thermus thermophilus 70S ribosome developed in silico. (2004) (41)
- Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. (2014) (41)
- Tertiary contacts control switching of the SAM-I riboswitch (2010) (41)
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution (2020) (40)
- Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. (2012) (37)
- Alignment/misalignment hypothesis for tRNA selection by the ribosome. (2006) (37)
- Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. (2016) (33)
- Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. (2011) (32)
- Towards structural classification of long non-coding RNAs. (2016) (28)
- New Paradigm for the Self-Consistent Modeling of Wave-Particle and Wave-Wave Interactions in the Saturation of Electromagnetically Driven Parametric Instabilities (1999) (28)
- Quantitative comparison of reduced-description particle-in-cell and quasilinear-Zakharov models for parametrically excited Langmuir turbulence (2000) (27)
- Simulating movement of tRNA through the ribosome during hybrid-state formation. (2013) (27)
- Domain motions of Argonaute, the catalytic engine of RNA interference (2007) (25)
- The effect of kinetic processes on Langmuir turbulence (2000) (24)
- cryo_fit: Democratization of Flexible Fitting for Cryo-EM. (2019) (23)
- Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection (2020) (21)
- Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression. (2015) (20)
- Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch (2019) (20)
- Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. (2015) (20)
- A magnesium-induced triplex pre-organizes the SAM-II riboswitch (2017) (19)
- Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model (2017) (17)
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. (2015) (16)
- Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle (2017) (14)
- Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch. (2017) (14)
- Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps (2020) (12)
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR. (2019) (11)
- 3 S : Shotgun secondary structure determination of long non-coding RNAs (2014) (10)
- Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages (2016) (9)
- Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein (2020) (9)
- Dynamics of riboswitches: Molecular simulations. (2014) (8)
- Large-scale simulations of the ribosome: a new landmark in computational biology (2006) (8)
- Dynamic views of ribosome function: Energy landscapes and ensembles (2011) (8)
- Elongation Factor-Tu switch I is a gate for aminoacyl-tRNA selection. (2020) (7)
- Getting to the bottom of lncRNA mechanism: structure–function relationships (2021) (6)
- Flipping through the genetic code: new developments in discrimination between cognate and near-cognate tRNAs and the effect of antibiotics. (2014) (6)
- Nonlinear coupling of lower hybrid waves to the kinetic low‐frequency plasma response in the auroral ionosphere (1995) (4)
- Molecular Dynamics Simulations of the Ribosome (2012) (4)
- Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome (2021) (4)
- Laying a foundation for laser-plasma modeling for the national ignition facility (2000) (3)
- Comparison of molecular dynamics and particle-in-cell simulations for strongly coupled plasmas (2000) (3)
- Quasi‐linear Zakharov simulations of Langmuir turbulence at rocket altitudes in the auroral ionosphere (2001) (3)
- Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation. (2021) (3)
- Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position (2017) (2)
- Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail (2021) (2)
- Stalking Structure in Plant Long Noncoding RNAs. (2019) (2)
- 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) (2015) (2)
- Molecular Dynamics Simulations of Ribosomes: Integrating Theory and Experiment (2014) (2)
- Using Computer Simulations to Study Decoding by the Ribosome (2006) (2)
- tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST) (2010) (1)
- Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. (2022) (1)
- Exploring the energy landscape of riboswitches using collective variables based on tertiary contacts. (2022) (1)
- Magnesium Dependence of the RNA Free Energy Landscape (2015) (1)
- Comparing Speed-of-Sight studies using rendered vs. natural images (2010) (1)
- Simulations of the Bacterial Ribosomal Decoding Switch (2010) (0)
- Explorer Trends and challenges in Computational RNA biology (2016) (0)
- Saturation of Langmuir decay instability collapse in reduced-description particle-in-cell and quasilinear-Zakharov simulations (1998) (0)
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting. (2022) (0)
- Structur eo fMet-Enkephali ni nExplici tAqueou sSolution Usin gReplic aExchang eMolecula rDynamics (2002) (0)
- Dynamic Mode Switching and Loosely Coupled Conformational Events Observed in Single Ribosomes (2009) (0)
- Simulations of the Ribosome Suggest Reversible Transitions and Parallel Pathways are Involved in the Large-Scale Functional Motions of tRNA During Translation (2010) (0)
- All-atom Models For RNA And Proteins: Simulating Folding And Function (2009) (0)
- All-atom homology structure of the Escherichia coli 30S ribosomal subunit (2002) (0)
- Polymer modelling accurately predicts three-dimensional chromosome reorganization with a seasonal coronavirus infection (2023) (0)
- Issue Information (2019) (0)
- Revealing the Energy Landscapes of Ribosome Function (2011) (0)
- Simulating nucleoprotein complexes: chromatin and ribosomes (2019) (0)
- Single Molecule Series A New View of Protein Synthesis: Mapping the Free Energy Landscape of the Ribosome Using Single-Molecule FRET (2010) (0)
- Simulating Movement of the Ribosome Head during Translocation (2017) (0)
- 9.5 Dynamics of Very Large Systems: The Ribosome (2012) (0)
- Ribosome hyper-swivel head domain motions are required for translocation and resetting. (2023) (0)
- A 4-Dimensional Human Genome Project: Accelerating the Next Generation of Biological Discovery (2021) (0)
- Functional Non-Coding RNA Coding Vascular Epigenetics: Chance and Necessity in Adaptation Reactions (2012) (0)
- Large-scale simulations of molecular machines: the ribosome (2015) (0)
- Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022) (2022) (0)
- High-throughput Mapping of Cotranscriptional Assembly of the 30S Ribosomal Subunit (2018) (0)
- Improved Quality Metrics for Association and Reproducibility in Chromatin Accessibility Data Using Mutual Information (2023) (0)
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution (2020) (0)
- Probing the Energy Landscape of Ribosome Function Through Simulation (2012) (0)
- Exaggerated Swivel Motions of the Small Subunit Head Domain are Required for tRNA Translocation through the Bacterial Ribosome (2018) (0)
- Information Processing by Nanomachines: Decoding by the Ribosome (2011) (0)
- Glass-Like Behavior of Magnesium Ions Inside RNA APTamers (2012) (0)
- New Insights Into “Plant Memories” (2016) (0)
- model structure of the T. thermophilus 70S ribosome, 30S subunit of 70S robosome. THIS FILE, 1TWT, CONTAINS ONLY MOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50S SUBUNIT IS IN THE PDB FILE 1TWV. (2004) (0)
- Going Big: Million Atom Simulations of Ribosomes and Billion Atom Simulations of Chromatin (2020) (0)
- Cryo-Em Structures of Ribosomal 80S Complexes with Termination Factors and Cricket Paralysis Virus Ires Reveal the Ires in the Translocated State (2015) (0)
- 35 The energy landscapes of ribosome function (2013) (0)
- 4D chromosome reconstruction elucidates the spatial reorganization of the mammalian X-chromosome (2021) (0)
- Heterogenous dynamics, connectivity and domain formation in polymer glasses: a fractal dimension analysis approach (2019) (0)
- Science on Tap 2020 (2020) (0)
- Resource Identification and Charact erization of a Class of MALAT 1-like Genomic Loci Graphical Abstract Highlights (2017) (0)
- Correction (1951) (0)
- Biochemical Studies of a Long Noncoding RNA Involved in Breast Cancer Biology (2012) (0)
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding. (2023) (0)
- Supercomputing in biology: towards understanding living systems in atomic detail (2010) (0)
- Faculty Opinions recommendation of Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome. (2015) (0)
- Chemical probing profiling of 2'-deoxyguanosine sensing RNA reveals magnesium ion-dependent conformational switching. (2023) (0)
- The shear viscosity of strongly coupled screened Coulomb systems (2000) (0)
- Correction for Kaushal et al., Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome (2015) (0)
- Task-specific saliency from sparse, hierarchical models of visual cortex compared to eye-tracking data for object detection in natural video sequences (2011) (0)
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