Sanbonmatsu, Karissa: search on Z-Library

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1

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

Xinying Shi, Prashant K. Khade, Karissa Y. Sanbonmatsu, Simpson Joseph

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 962 KB

english, 2012

2

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

Kim, Doo Nam, Thiel, Bernhard C., Mrozowich, Tyler, Hennelly, Scott P., Hofacker, Ivo L., Patel, Trushar R., Sanbonmatsu, Karissa Y.

Journal:

Nature Communications

Year:

2020

Language:

english

File:

PDF, 6.26 MB

english, 2020

3

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

Roy, Susmita, Hennelly, Scott P, Lammert, Heiko, Onuchic, José N, Sanbonmatsu, Karissa Y

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 2.99 MB

english, 2019

4

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Hayes, Ryan L., Noel, Jeffrey K., Mandic, Ana, Whitford, Paul C., Sanbonmatsu, Karissa Y., Mohanty, Udayan, Onuchic, José N.

Journal:

Physical Review Letters

Year:

2015

Language:

english

File:

PDF, 240 KB

english, 2015

5

Biochemical Studies of a Long Noncoding RNA Involved in Breast Cancer Biology

Novikova, Irina V., Hennelly, Scott P., Sanbonmatsu, Karissa Y.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 52 KB

english, 2012

6

Magnesium Dependence of the RNA Free Energy Landscape

Hayes, Ryan L., Noel, Jeffrey K., Mandic, Ana, Whitford, Paul C., Sanbonmatsu, Karissa Y., Mohanty, Udayan, Onuchic, José N.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

7

Exaggerated Swivel Motions of the Small Subunit Head Domain are Required for tRNA Translocation through the Bacterial Ribosome

Nishima, Wataru, Blanchard, Scott C., Sanbonmatsu, Karissa Y.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 39 KB

english, 2018

8

Revealing the Energy Landscapes of Ribosome Function

Whitford, Paul C., Spahn, Christian M.T., Blanchard, Scott C., Onuchic, Jose' N., Sanbonmatsu, Karissa Y.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 37 KB

english, 2011

9

Excited states of ribosome translocation revealed through integrative molecular modeling

Paul C. Whitford, Aqeel Ahmed, Yanan Yu, Scott P. Hennelly, Florence Tama, Christian M. T. Spahn, José N. Onuchic and Karissa Y. Sanbonmatsu

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.87 MB

english, 2011

10

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

Whitford, Paul C., Sanbonmatsu, Karissa Y.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 2.02 MB

english, 2013

11

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

Bascom, Gavin D, Sanbonmatsu, Karissa Y., Schlick, Tamar

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 4.71 MB

english, 2016

12

Glass-Like Behavior of Magnesium Ions Inside RNA APTamers

Hayes, Ryan L., Onuchic, Jose, Noel, Jeff, Sanbonmatsu, Karissa, Mohanty, Udayan

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 37 KB

english, 2012

13

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

Novikova, Irina V., Hennelly, Scott P., Sanbonmatsu, Karissa Y.

Journal:

BioArchitecture

Year:

2012

Language:

english

File:

PDF, 2.01 MB

english, 2012

14

Going Big: Million Atom Simulations of Ribosomes and Billion Atom Simulations of Chromatin

Sanbonmatsu, Karissa Y.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 38 KB

2020

15

Tackling Structures of Long Noncoding RNAs

Novikova, Irina, Hennelly, Scott, Sanbonmatsu, Karissa

Journal:

International Journal of Molecular Sciences

Year:

2013

Language:

english

File:

PDF, 815 KB

english, 2013

16

Reduced Model Captures Mg2+-RNA Interaction Free Energy of Riboswitches

Hayes, Ryan L., Noel, Jeffrey K., Whitford, Paul C., Mohanty, Udayan, Sanbonmatsu, Karissa Y., Onuchic, José N.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 890 KB

english, 2014

17

Dynamics of riboswitches: Molecular simulations

Sanbonmatsu, Karissa Y.

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Year:

2014

Language:

english

File:

PDF, 295 KB

english, 2014

18

Simulating Movement of the Ribosome Head during Translocation

Sanbonmatsu, Karissa Y., Nishima, Wataru

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 43 KB

english, 2017

19

Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome

Whitford, Paul C., Onuchic, José N., Sanbonmatsu, Karissa Y.

Journal:

Journal of the American Chemical Society

Year:

2010

Language:

english

File:

PDF, 940 KB

english, 2010

20

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch

Hayes, Ryan L., Noel, Jeffrey K., Mohanty, Udayan, Whitford, Paul C., Hennelly, Scott P., Onuchic, José N., Sanbonmatsu, Karissa Y.

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 3.53 MB

english, 2012

21

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

Kim, Doo Nam, Sanbonmatsu, Karissa

Journal:

Bioscience Reports

Year:

2017

Language:

english

File:

PDF, 545 KB

english, 2017

22

35 The energy landscapes of ribosome function

Noel, Jeffrey K., Sanbonmatsu, Karissa Y., Whitford, Paul C.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 99 KB

english, 2013

23

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

Roy, Susmita, Onuchic, José N., Sanbonmatsu, Karissa Y.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 3.52 MB

english, 2017

24

cryo_fit: Democratization of Flexible Fitting for Cryo-EM

Kim, Doo Nam, Moriarty, Nigel W., Kirmizialtin, Serdal, Afonine, Pavel V., Poon, Billy, Sobolev, Oleg V., Adams, Paul D., Sanbonmatsu, Karissa

Journal:

Journal of Structural Biology

Year:

2019

Language:

english

File:

PDF, 3.35 MB

english, 2019

25

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

Colby D. Stoddard, Rebecca K. Montange, Scott P. Hennelly, Robert P. Rambo, Karissa Y. Sanbonmatsu, Robert T. Batey

Journal:

Year:

2010

Language:

english

File:

PDF, 1.56 MB

english, 2010

26

Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

Gulay, Suna P., Bista, Sujal, Varshney, Amitabh, Kirmizialtin, Serdal, Sanbonmatsu, Karissa Y., Dinman, Jonathan D.

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 6.32 MB

english, 2017

27

Computational studies of molecular machines: the ribosome

Karissa Y Sanbonmatsu

Journal:

Current Opinion in Structural Biology

Year:

2012

Language:

english

File:

PDF, 1.63 MB

english, 2012

28

Probing the Energy Landscape of Ribosome Function Through Simulation

Whitford, Paul C., Sanbonmatsu, Karissa

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 65 KB

english, 2012

29

High-throughput Mapping of Cotranscriptional Assembly of the 30S Ribosomal Subunit

Yang, Feng, Kunde, Yuliya A., Hennelly, Scott P., Sanbonmatsu, Karissa Y., Starkenburg, Shawn R., Goodwin, Peter M.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 44 KB

english, 2018

30

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

Novikova, Irina V., Dharap, Ashutosh, Hennelly, Scott P., Sanbonmatsu, Karissa Y.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.78 MB

english, 2013

31

Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES

Muhs, Margarita, Hilal, Tarek, Mielke, Thorsten, Skabkin, Maxim A., Sanbonmatsu, Karissa Y., Pestova, Tatyana V., Spahn, Christian M.T.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.27 MB

english, 2015

32

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Hawkes, Emily J., Hennelly, Scott P., Novikova, Irina V., Irwin, Judith A., Dean, Caroline, Sanbonmatsu, Karissa Y.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.62 MB

english, 2016

33

Biomolecular dynamics: order–disorder transitions and energy landscapes

Whitford, Paul C, Sanbonmatsu, Karissa Y, Onuchic, José N

Journal:

Reports on Progress in Physics

Year:

2012

Language:

english

File:

PDF, 2.61 MB

english, 2012

34

[ACM Press the eighteenth ACM SIGSOFT international symposium - Santa Fe, New Mexico, USA (2010.11.07-2010.11.11)] Proceedings of the eighteenth ACM SIGSOFT international symposium on Foundations of software engineering - FSE '10 - Supercomputing in biology

Sanbonmatsu, Karissa Y.

Year:

2010

Language:

english

File:

PDF, 332 KB

english, 2010

35

Towards structural classification of long non-coding RNAs

Sanbonmatsu, Karissa

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Year:

2015

Language:

english

File:

PDF, 179 KB

english, 2015

36

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

Zhang, Bin, Mao, Yuntao S., Diermeier, Sarah D., Novikova, Irina V., Nawrocki, Eric P., Jones, Tom A., Lazar, Zsolt, Tung, Chang-Shung, Luo, Weijun, Eddy, Sean R., Sanbonmatsu, Karissa Y., Spector, Da

Journal:

Year:

2017

Language:

english

File:

PDF, 5.18 MB

english, 2017

37

cryo_fit: Democratization of Flexible Fitting for Cryo-EM

Kim, Doo Nam, Moriarty, Nigel W., Kirmizialtin, Serdal, Afonine, Pavel V., Poon, Billy, Sobolev, Oleg V., Adams, Paul D., Sanbonmatsu, Karissa

Journal:

Journal of Structural Biology

Year:

2019

File:

PDF, 3.35 MB

2019

38

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

Aqeel Ahmed, Paul C. Whitford, Karissa Y. Sanbonmatsu, Florence Tama

Journal:

Journal of Structural Biology

Year:

2012

Language:

english

File:

PDF, 1.41 MB

english, 2012

39

Key Intermolecular Interactions in the E. coli 70S Ribosome Revealed by Coarse-Grained Analysis

Zhang, Zhiyong, Sanbonmatsu, Karissa Y., Voth, Gregory A.

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 4.52 MB

english, 2011

40

Molecular Dynamics Simulations of Ribosomes: Integrating Theory and Experiment

Kirmizialtin, Serdal, Sanbonmatsu, Karissa Y.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 43 KB

english, 2014

41

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

Morse, Justin C., Girodat, Dylan, Burnett, Benjamin J., Holm, Mikael, Altman, Roger B., Sanbonmatsu, Karissa Y., Wieden, Hans-Joachim, Blanchard, Scott C.

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

Language:

english

File:

PDF, 1.95 MB

english, 2020

42

Flipping through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics

Sanbonmatsu, Karissa Y.

Journal:

Journal of Molecular Biology

Year:

2014

Language:

english

File:

PDF, 188 KB

english, 2014

43

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position

Liu, Wei, Shin, Dongwon, Ng, Martin, Sanbonmatsu, Karissa, Tor, Yitzhak, Cooperman, Barry

Journal:

Year:

2017

Language:

english

File:

PDF, 1.62 MB

english, 2017

44

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

Novikova, Irina V., Hennelly, Scott P., Tung, Chang-Shung, Sanbonmatsu, Karissa Y.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 2.31 MB

english, 2013

45

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

Whitford, Paul C., Blanchard, Scott C., Cate, Jamie H. D., Sanbonmatsu, Karissa Y., Chen, Shi-Jie

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.85 MB

english, 2013

46

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps

Kim, Doo Nam, Gront, Dominik, Sanbonmatsu, Karissa Y.

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 3.10 MB

2020

47

Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression

Krishnamurthy, Malathy, Hennelly, Scott P., Dale, Taraka, Starkenburg, Shawn R., Martí-Arbona, Ricardo, Fox, David T., Twary, Scott N., Sanbonmatsu, Karissa Y., Unkefer, Clifford J.

Journal:

ACS Synthetic Biology

Year:

2015

Language:

english

File:

PDF, 2.05 MB

english, 2015

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