Sarah A Woodson. Curr Opin Chem Biol 2005
Times Cited: 247
Times Cited: 247
Times Cited
Times Co-cited
Similarity
Ions and RNA folding.
David E Draper, Dan Grilley, Ana Maria Soto. Annu Rev Biophys Biomol Struct 2005
David E Draper, Dan Grilley, Ana Maria Soto. Annu Rev Biophys Biomol Struct 2005
28
Understanding nucleic acid-ion interactions.
Jan Lipfert, Sebastian Doniach, Rhiju Das, Daniel Herschlag. Annu Rev Biochem 2014
Jan Lipfert, Sebastian Doniach, Rhiju Das, Daniel Herschlag. Annu Rev Biochem 2014
22
RNA folding: conformational statistics, folding kinetics, and ion electrostatics.
Shi-Jie Chen. Annu Rev Biophys 2008
Shi-Jie Chen. Annu Rev Biophys 2008
20
RNA folding: thermodynamic and molecular descriptions of the roles of ions.
David E Draper. Biophys J 2008
David E Draper. Biophys J 2008
19
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides.
G S Manning. Q Rev Biophys 1978
G S Manning. Q Rev Biophys 1978
18
Charge density of divalent metal cations determines RNA stability.
Eda Koculi, Changbong Hyeon, D Thirumalai, Sarah A Woodson. J Am Chem Soc 2007
Eda Koculi, Changbong Hyeon, D Thirumalai, Sarah A Woodson. J Am Chem Soc 2007
15
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
Alberto Pérez, Iván Marchán, Daniel Svozil, Jiri Sponer, Thomas E Cheatham, Charles A Laughton, Modesto Orozco. Biophys J 2007
Alberto Pérez, Iván Marchán, Daniel Svozil, Jiri Sponer, Thomas E Cheatham, Charles A Laughton, Modesto Orozco. Biophys J 2007
15
Mfold web server for nucleic acid folding and hybridization prediction.
Michael Zuker. Nucleic Acids Res 2003
Michael Zuker. Nucleic Acids Res 2003
15
Predicting ion binding properties for RNA tertiary structures.
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2010
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2010
29
Salt contribution to RNA tertiary structure folding stability.
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2011
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2011
27
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
T Xia, J SantaLucia, M E Burkard, R Kierzek, S J Schroeder, X Jiao, C Cox, D H Turner. Biochemistry 1998
T Xia, J SantaLucia, M E Burkard, R Kierzek, S J Schroeder, X Jiao, C Cox, D H Turner. Biochemistry 1998
14
13
Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte.
Zhi-Jie Tan, Shi-Jie Chen. J Chem Phys 2005
Zhi-Jie Tan, Shi-Jie Chen. J Chem Phys 2005
13
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
Ryan L Hayes, Jeffrey K Noel, Udayan Mohanty, Paul C Whitford, Scott P Hennelly, José N Onuchic, Karissa Y Sanbonmatsu. J Am Chem Soc 2012
Ryan L Hayes, Jeffrey K Noel, Udayan Mohanty, Paul C Whitford, Scott P Hennelly, José N Onuchic, Karissa Y Sanbonmatsu. J Am Chem Soc 2012
22
Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.
Li-Zhen Sun, Dong Zhang, Shi-Jie Chen. Annu Rev Biophys 2017
Li-Zhen Sun, Dong Zhang, Shi-Jie Chen. Annu Rev Biophys 2017
20
Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions.
Ana Maria Soto, Vinod Misra, David E Draper. Biochemistry 2007
Ana Maria Soto, Vinod Misra, David E Draper. Biochemistry 2007
13
Cations in charge: magnesium ions in RNA folding and catalysis.
Jessica C Bowman, Timothy K Lenz, Nicholas V Hud, Loren Dean Williams. Curr Opin Struct Biol 2012
Jessica C Bowman, Timothy K Lenz, Nicholas V Hud, Loren Dean Williams. Curr Opin Struct Biol 2012
12
Coarse-grained model for predicting RNA folding thermodynamics.
Natalia A Denesyuk, D Thirumalai. J Phys Chem B 2013
Natalia A Denesyuk, D Thirumalai. J Phys Chem B 2013
16
Importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg2+ interactions.
Dan Grilley, Vinod Misra, Gokhan Caliskan, David E Draper. Biochemistry 2007
Dan Grilley, Vinod Misra, Gokhan Caliskan, David E Draper. Biochemistry 2007
19
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.
In Suk Joung, Thomas E Cheatham. J Phys Chem B 2008
In Suk Joung, Thomas E Cheatham. J Phys Chem B 2008
11
RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.
Serdal Kirmizialtin, Suzette A Pabit, Steve P Meisburger, Lois Pollack, Ron Elber. Biophys J 2012
Serdal Kirmizialtin, Suzette A Pabit, Steve P Meisburger, Lois Pollack, Ron Elber. Biophys J 2012
16
Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length.
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2006
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2006
11
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
Marc Parisien, François Major. Nature 2008
Marc Parisien, François Major. Nature 2008
11
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.
Marie Zgarbová, Michal Otyepka, Jiří Sponer, Arnošt Mládek, Pavel Banáš, Thomas E Cheatham, Petr Jurečka. J Chem Theory Comput 2011
Marie Zgarbová, Michal Otyepka, Jiří Sponer, Arnošt Mládek, Pavel Banáš, Thomas E Cheatham, Petr Jurečka. J Chem Theory Comput 2011
11
A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect.
Ya-Zhou Shi, Feng-Hua Wang, Yuan-Yan Wu, Zhi-Jie Tan. J Chem Phys 2014
Ya-Zhou Shi, Feng-Hua Wang, Yuan-Yan Wu, Zhi-Jie Tan. J Chem Phys 2014
27
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.
Yu Bai, Max Greenfeld, Kevin J Travers, Vincent B Chu, Jan Lipfert, Sebastian Doniach, Daniel Herschlag. J Am Chem Soc 2007
Yu Bai, Max Greenfeld, Kevin J Travers, Vincent B Chu, Jan Lipfert, Sebastian Doniach, Daniel Herschlag. J Am Chem Soc 2007
10
A compact RNA tertiary structure contains a buried backbone-K+ complex.
Graeme L Conn, Apostolos G Gittis, Eaton E Lattman, Vinod K Misra, David E Draper. J Mol Biol 2002
Graeme L Conn, Apostolos G Gittis, Eaton E Lattman, Vinod K Misra, David E Draper. J Mol Biol 2002
10
Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.
Yuan-Yan Wu, Zhong-Liang Zhang, Jin-Si Zhang, Xiao-Long Zhu, Zhi-Jie Tan. Nucleic Acids Res 2015
Yuan-Yan Wu, Zhong-Liang Zhang, Jin-Si Zhang, Xiao-Long Zhu, Zhi-Jie Tan. Nucleic Acids Res 2015
25
11
Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.
Ryan L Hayes, Jeffrey K Noel, Ana Mandic, Paul C Whitford, Karissa Y Sanbonmatsu, Udayan Mohanty, José N Onuchic. Phys Rev Lett 2015
Ryan L Hayes, Jeffrey K Noel, Ana Mandic, Paul C Whitford, Karissa Y Sanbonmatsu, Udayan Mohanty, José N Onuchic. Phys Rev Lett 2015
28
RNA 3D structure prediction by using a coarse-grained model and experimental data.
Zhen Xia, David R Bell, Yue Shi, Pengyu Ren. J Phys Chem B 2013
Zhen Xia, David R Bell, Yue Shi, Pengyu Ren. J Phys Chem B 2013
19
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Michal J Boniecki, Grzegorz Lach, Wayne K Dawson, Konrad Tomala, Pawel Lukasz, Tomasz Soltysinski, Kristian M Rother, Janusz M Bujnicki. Nucleic Acids Res 2016
Michal J Boniecki, Grzegorz Lach, Wayne K Dawson, Konrad Tomala, Pawel Lukasz, Tomasz Soltysinski, Kristian M Rother, Janusz M Bujnicki. Nucleic Acids Res 2016
10
Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs.
Alexander Serganov, Yu-Ren Yuan, Olga Pikovskaya, Anna Polonskaia, Lucy Malinina, Anh Tuân Phan, Claudia Hobartner, Ronald Micura, Ronald R Breaker, Dinshaw J Patel. Chem Biol 2004
Alexander Serganov, Yu-Ren Yuan, Olga Pikovskaya, Anna Polonskaia, Lucy Malinina, Anh Tuân Phan, Claudia Hobartner, Ronald Micura, Ronald R Breaker, Dinshaw J Patel. Chem Biol 2004
9
Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry.
Roland K O Sigel, Anna Marie Pyle. Chem Rev 2007
Roland K O Sigel, Anna Marie Pyle. Chem Rev 2007
9
Electrostatics of nanosystems: application to microtubules and the ribosome.
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
9
Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations.
S L Heilman-Miller, D Thirumalai, S A Woodson. J Mol Biol 2001
S L Heilman-Miller, D Thirumalai, S A Woodson. J Mol Biol 2001
9
Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures.
Dan Grilley, Ana Maria Soto, David E Draper. Proc Natl Acad Sci U S A 2006
Dan Grilley, Ana Maria Soto, David E Draper. Proc Natl Acad Sci U S A 2006
10
Ion counting from explicit-solvent simulations and 3D-RISM.
George M Giambaşu, Tyler Luchko, Daniel Herschlag, Darrin M York, David A Case. Biophys J 2014
George M Giambaşu, Tyler Luchko, Daniel Herschlag, Darrin M York, David A Case. Biophys J 2014
15
Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.
Huimin Chen, Steve P Meisburger, Suzette A Pabit, Julie L Sutton, Watt W Webb, Lois Pollack. Proc Natl Acad Sci U S A 2012
Huimin Chen, Steve P Meisburger, Suzette A Pabit, Julie L Sutton, Watt W Webb, Lois Pollack. Proc Natl Acad Sci U S A 2012
9
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.
Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V Demidov, Natalia E Broude, Nikolay V Dokholyan. RNA 2008
Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V Demidov, Natalia E Broude, Nikolay V Dokholyan. RNA 2008
9
31
Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations.
Olof Allnér, Lennart Nilsson, Alessandra Villa. J Chem Theory Comput 2012
Olof Allnér, Lennart Nilsson, Alessandra Villa. J Chem Theory Comput 2012
9
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
9
14
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.